Gene expression analysis of combined treatment of metastatic breast cancer

Study description

This study looks at how a combination of pembrolizumab, exemestane, and leuprolide affects the immune environment in premenopausal women with advanced breast cancer. It tracks changes in immune-related gene expression before and after treatment in 15 patients.

Work method illustrated by a flowchart

Untidy –> Tidy data

  1. Each variable is saved in its own column.
  2. Each observation is saved in its own row.
  3. Each “type” of observation is stored in a single table.
# Untidy single patient dataset
print(read.csv(here("data/01_dat_load_pre_data_GSM8152441.csv")))
                                 X.Header.
1                          FileVersion,2.0
2                 SoftwareVersion,2.3.0.44
3                          SystemType,Gen3
4                                </Header>
5                      <Sample_Attributes>
6                                 ID,01002
7                      Owner,Administrator
8                                Comments,
9                            Date,20220128
10                  GeneRLF,NS_IO_360_v1.0
11                       SystemAPF,n6_vDV1
12                  AssayType,Non Specific
13                    </Sample_Attributes>
14                       <Lane_Attributes>
15                                    ID,4
16                            FovCount,194
17                          FovCounted,194
18                     ScannerID,1706P0203
19                         StagePosition,1
20                     BindingDensity,0.38
21           CartridgeID,30102613280522-01
22         CartridgeBarcode,30102613280522
23                      </Lane_Attributes>
24                          <Code_Summary>
25          CodeClass,Name,Accession,Count
26          Endogenous,CCNO,NM_021147.4,14
27          Endogenous,MYC,NM_002467.3,632
28         Endogenous,CD79A,NM_001783.3,10
29         Endogenous,FSTL3,NM_005860.2,45
30     Endogenous,VCAN,NM_001126336.2,1141
31        Endogenous,CX3CL1,NM_002996.3,59
32        Endogenous,ERBB2,NM_004448.2,315
33    Endogenous,FAM124B,NM_001122779.1,21
34        Endogenous,AKT1,NM_005163.2,1050
35           Endogenous,KDR,NM_002253.2,79
36        Endogenous,EGF,NM_001178130.2,78
37   Endogenous,MAGEA12,NM_001166386.1,125
38         Endogenous,IFNA1,NM_024013.1,65
39      Endogenous,TGFB3,NM_001329938.1,75
40     Endogenous,MFGE8,NM_001114614.1,528
41         Endogenous,CXCL2,NM_002089.1,87
42        Endogenous,CCND2,NM_001759.2,144
43      Endogenous,PDZK1IP1,NM_005764.3,27
44          Endogenous,JAG2,NM_002226.4,38
45         Endogenous,C5,NM_001317163.1,21
46      Endogenous,CD79B,NM_001039933.1,13
47         Endogenous,CXCR2,NM_001557.3,17
48        Endogenous,PSMB10,NM_002801.3,79
49      Endogenous,ZEB1,NM_001128128.2,138
50         Endogenous,ANLN,NM_018685.2,121
51          Endogenous,TAF3,NM_031923.3,19
52     Endogenous,CD276,NM_001024736.1,939
53         Endogenous,ICAM1,NM_000201.2,70
54          Endogenous,IL16,NM_004513.4,52
55         Endogenous,CXCL3,NM_002090.2,17
56          Endogenous,PRR5,NM_015366.3,48
57          Endogenous,CTSW,NM_001335.3,13
58     Endogenous,CXCR4,NM_001008540.1,298
59       Endogenous,IFNGR2,NM_005534.3,483
60        Endogenous,CDH11,NM_001797.2,725
61      Endogenous,COL6A3,NM_004369.3,1878
62          Endogenous,GZMK,NM_002104.2,17
63         Endogenous,IRF2,NM_002199.3,165
64       Endogenous,RPL7A,NM_000972.2,2589
65       Endogenous,GPR160,NM_014373.1,198
66          Endogenous,MICA,NM_000247.1,52
67        Endogenous,TAPBPL,NM_018009.4,88
68       Endogenous,CXCL14,NM_004887.4,167
69       Endogenous,CD14,NM_001174105.1,88
70       Endogenous,IL18,NM_001243211.1,65
71       Endogenous,CLEC14A,NM_175060.1,24
72        Endogenous,HMGB1,NM_002128.5,102
73         Endogenous,KIF2C,NM_006845.2,64
74       Endogenous,RNLS,NM_001031709.2,35
75     Endogenous,RPTOR,NM_001163034.1,126
76         Endogenous,CD68,NM_001251.2,109
77          Endogenous,CCL13,NM_005408.2,9
78         Endogenous,CYBB,NM_000397.3,169
79       Endogenous,PLA2G2A,NM_000300.2,16
80      Endogenous,FGF13,NM_001139498.1,22
81         Endogenous,CNTFR,NM_147164.2,15
82      Endogenous,CD244,NM_001166663.1,17
83        Endogenous,CSF2RB,NM_000395.2,17
84       Endogenous,MAP3K7,NM_003188.3,278
85         Endogenous,FASLG,NM_000639.2,16
86         Endogenous,CD209,NM_021155.2,13
87         Endogenous,IRF7,NM_004029.2,465
88     Endogenous,PTCD2,NM_001284403.1,117
89       Endogenous,PIK3R2,NM_005027.3,382
90        Endogenous,LILRA5,NM_181879.2,23
91         Endogenous,IL32,NM_004221.4,297
92      Endogenous,CCND3,NM_001136017.2,45
93        Endogenous,BIRC5,NM_001168.2,198
94        Endogenous,LGALS9,NM_002308.3,42
95     Endogenous,RASAL1,NM_001193520.1,39
96      Endogenous,PDCD1LG2,NM_025239.3,39
97          Endogenous,IL11,NM_000641.3,51
98          Endogenous,PRKX,NM_005044.4,19
99       Endogenous,SNCA,NM_001146055.1,16
100    Endogenous,ADGRE1,NM_001256252.1,16
101       Endogenous,PSMB9,NM_002800.4,115
102     Endogenous,RUNX3,NM_001031680.2,26
103    Endogenous,PGPEP1,NM_001300927.1,33
104        Endogenous,MELK,NM_014791.2,160
105      Endogenous,ISG15,NM_005101.3,1631
106   Endogenous,EIF2B4,NM_001034116.1,117
107        Endogenous,IRF9,NM_006084.4,548
108         Endogenous,IL1A,NM_000575.3,32
109     Endogenous,FCRL2,NM_001159488.1,13
110   Endogenous,EIF4EBP1,NM_004095.3,1412
111       Endogenous,LTBP1,NM_000627.3,160
112        Endogenous,CD40LG,NM_000074.2,9
113     Endogenous,HEY1,NM_001040708.1,166
114    Endogenous,HLA-DQA1,NM_002122.3,295
115        Endogenous,PRLR,NM_000949.5,601
116 Endogenous,TNFRSF11A,NM_001270949.1,40
117         Endogenous,AREG,NM_001657.3,57
118        Endogenous,BBC3,NM_014417.4,180
119         Endogenous,EDN1,NM_001955.2,36
120      Endogenous,PARP12,NM_022750.3,264
121    Endogenous,PIK3CG,NM_001282426.1,38
122          Endogenous,IL4,NM_172348.1,13
123        Endogenous,F2RL1,NM_005242.4,48
124        Endogenous,CXCL6,NM_002993.3,20
125      Endogenous,TNFSF18,NM_005092.3,17
126         Endogenous,JAK3,NM_000215.2,44
127         Endogenous,NKG7,NM_005601.3,33
128       Endogenous,TAPBP,NM_003190.4,533
129        Endogenous,MTOR,NM_004958.3,200
130         Endogenous,SELP,NM_003005.3,13
131       Endogenous,HLA-E,NM_005516.5,670
132        Endogenous,GOT1,NM_002079.2,265
133    Endogenous,SMAP1,NM_001044305.2,157
134      Endogenous,CDKN1A,NM_000389.2,430
135        Endogenous,CD45RA,NM_002838.4,8
136        Endogenous,HNF1A,NM_000545.6,12
137       Endogenous,TICAM1,NM_182919.3,36
138        Endogenous,C1QA,NM_015991.3,100
139      Endogenous,CD86,NM_001206924.1,25
140       Endogenous,ITGA4,NM_000885.5,108
141     Endogenous,ROR2,NM_001318204.1,129
142        Endogenous,WNT7B,NM_058238.2,97
143        Endogenous,FLT1,NM_002019.4,381
144       Endogenous,CTAG1B,NM_001327.2,58
145       Endogenous,CLEC7A,NM_197954.2,83
146      Endogenous,TNFRSF4,NM_003327.3,18
147       Endogenous,MS4A6A,NM_152852.2,27
148      Endogenous,ANGPT2,NM_001147.2,113
149    Endogenous,APH1B,NM_001145646.1,169
150      Endogenous,RORC,NM_001001523.1,56
151  Endogenous,NECTIN2,NM_001042724.1,286
152         Endogenous,DPP4,NM_001935.3,31
153        Endogenous,CCL2,NM_002982.3,789
154         Endogenous,NF1,NM_000267.3,168
155     Endogenous,S100A9,NM_002965.3,1519
156     Endogenous,NFKBIA,NM_020529.2,1304
157   Endogenous,BNIP3L,NM_001330491.1,267
158         Endogenous,CST2,NM_001322.2,24
159       Endogenous,APOL6,NM_030641.3,178
160     Endogenous,BRD4,NM_001330384.1,320
161     Endogenous,SLC16A1,NM_003051.3,264
162         Endogenous,THBD,NM_000361.2,35
163        Endogenous,TIGIT,NM_173799.2,15
164         Endogenous,VSIR,NM_022153.1,17
165      Endogenous,TRIM21,NM_003141.3,118
166         Endogenous,NBN,NM_002485.4,371
167         Endogenous,WNT4,NM_030761.4,15
168        Endogenous,CXCL8,NM_000584.3,54
169         Endogenous,FGF9,NM_002010.2,11
170        Endogenous,C5AR1,NM_001736.3,17
171     Endogenous,TNFRSF1B,NM_001066.2,25
172     Endogenous,HLA-DRB5,NM_002125.3,17
173       Endogenous,GLUL,NM_002065.6,1920
174        Endogenous,LY9,NM_001033667.2,7
175        Endogenous,TAP1,NM_000593.5,295
176       Endogenous,IFIH1,NM_022168.3,778
177   Endogenous,DEPTOR,NM_001283012.1,138
178       Endogenous,CSF1R,NM_005211.3,186
179        Endogenous,MARCO,NM_006770.3,21
180    Endogenous,NFIL3,NM_001289999.1,133
181     Endogenous,IKBKG,NM_001099856.4,46
182      Endogenous,CD58,NM_001144822.1,36
183        Endogenous,LOXL2,NM_002318.2,64
184        Endogenous,SPRY4,NM_030964.3,42
185         Endogenous,NFAM1,NM_145912.5,9
186          Endogenous,SYK,NM_003177.5,61
187        Endogenous,COMP,NM_000095.2,314
188      Endogenous,IFI6,NM_002038.3,24292
189  Endogenous,RASGRF1,NM_001145648.1,329
190    Endogenous,HDAC5,NM_001015053.1,101
191        Endogenous,BAMBI,NM_012342.2,43
192       Endogenous,MAGEC1,NM_005462.4,12
193          Endogenous,FYN,NM_002037.5,89
194    Endogenous,TNFSF4,NM_001297562.1,40
195        Endogenous,CD274,NM_014143.3,31
196       Endogenous,PRKACB,NM_182948.2,47
197       Endogenous,IFIT2,NM_001547.4,164
198        Endogenous,PPARG,NM_005037.5,31
199        Endogenous,PTEN,NM_000314.6,178
200        Endogenous,FOXP3,NM_014009.3,20
201   Endogenous,SREBF1,NM_001005291.1,870
202      Endogenous,CD36,NM_001001548.2,99
203        Endogenous,AXIN1,NM_181050.1,83
204        Endogenous,KLRK1,NM_007360.3,19
205        Endogenous,GBP1,NM_002053.2,108
206      Endogenous,CXCL11,NM_005409.4,175
207      Endogenous,CXCL10,NM_001565.3,770
208       Endogenous,RIPK1,NM_003804.3,157
209           Endogenous,REN,NM_000537.3,6
210      Endogenous,PRF1,NM_001083116.1,17
211  Endogenous,EIF2AK2,NM_001135652.2,997
212          Endogenous,LIF,NM_002309.4,43
213        Endogenous,BRD3,NM_007371.3,225
214       Endogenous,IGF2R,NM_000876.2,133
215         Endogenous,FPR1,NM_002029.3,26
216      Endogenous,DUSP5,NM_004419.3,1036
217      Endogenous,APC,NM_001127510.2,394
218       Endogenous,HDAC3,NM_003883.3,224
219      Endogenous,CES3,NM_001185176.1,55
220       Endogenous,OAS2,NM_016817.2,1380
221    Endogenous,HDAC11,NM_001330636.1,51
222      Endogenous,THBS1,NM_003246.2,1778
223      Endogenous,SLC11A1,NM_000578.3,41
224   Endogenous,MAGEA3/A6,NM_005362.3,470
225      Endogenous,ARID1A,NM_006015.4,316
226         Endogenous,CD48,NM_001778.3,26
227         Endogenous,GZMA,NM_006144.3,13
228      Endogenous,ICOSLG,NM_015259.4,130
229       Endogenous,PIK3R5,NM_014308.3,37
230         Endogenous,GZMM,NM_005317.2,13
231       Endogenous,WNT5A,NM_003392.3,109
232         Endogenous,TLR4,NR_024168.1,79
233          Endogenous,GZMB,NM_004131.4,8
234    Endogenous,PARP9,NM_001146103.1,445
235     Endogenous,LY96,NM_001195797.1,154
236       Endogenous,RAD50,NM_005732.3,612
237      Endogenous,MX1,NM_001144925.2,451
238       Endogenous,CENPF,NM_016343.3,126
239          Endogenous,SELL,NM_000655.4,9
240     Endogenous,TNFSF10,NM_003810.3,378
241   Endogenous,IL12RB2,NM_001319233.1,23
242        Endogenous,CXCL9,NM_002416.2,22
243         Endogenous,TRAT1,NM_016388.3,5
244         Endogenous,STC1,NM_003155.2,61
245        Endogenous,IL2RB,NM_000878.2,18
246    Endogenous,LILRB4,NM_001278426.3,44
247          Endogenous,SOX2,NM_003106.2,9
248       Endogenous,HCK,NM_001172129.1,55
249     Endogenous,WNT2B,NM_001291880.1,20
250         Endogenous,IL1B,NM_000576.2,19
251         Endogenous,TLR1,NM_003263.3,60
252        Endogenous,CCL22,NM_002990.3,15
253        Endogenous,ICAM2,NM_000873.3,19
254      Endogenous,MAP3K12,NM_006301.3,59
255        Endogenous,JAG1,NM_000214.2,119
256     Endogenous,CCL3/L1,NM_021006.5,122
257        Endogenous,SOCS1,NM_003745.1,39
258        Endogenous,BCL2,NM_000633.2,198
259   Endogenous,MAP3K8,NM_001244134.1,213
260         Endogenous,MMP1,NM_002421.2,47
261       Endogenous,CMKLR1,NM_004072.2,40
262     Endogenous,TNFRSF17,NM_001192.2,10
263         Endogenous,TLR8,NM_138636.4,21
264        Endogenous,TPM1,NM_000366.5,580
265      Endogenous,CXorf36,NM_024689.2,48
266     Endogenous,NLRP3,NM_001079821.2,16
267   Endogenous,DEFB134,NM_001302695.1,16
268     Endogenous,HLA-DQA2,NM_020056.4,25
269    Endogenous,CX3CR1,NM_001171171.1,11
270         Endogenous,APLNR,NM_005161.4,7
271      Endogenous,MXI1,NM_001008541.1,88
272         Endogenous,FZD9,NM_003508.2,16
273      Endogenous,COL4A5,NM_000495.4,101
274         Endogenous,FCAR,NM_133278.2,13
275        Endogenous,BRCA2,NM_000059.3,85
276       Endogenous,SFRP4,NM_003014.2,163
277         Endogenous,TLR3,NM_003265.2,89
278        Endogenous,IL2RG,NM_000206.1,21
279      Endogenous,CD84,NM_001184879.1,60
280    Endogenous,HLA-DPA1,NM_033554.2,330
281     Endogenous,RBL2,NM_001323611.1,427
282       Endogenous,CCL18,NM_002988.3,135
283     Endogenous,IRF3,NM_001197122.1,126
284       Endogenous,TNFRSF8,NM_001243.3,4
285       Endogenous,KIR3DL2,NM_006737.2,5
286      Endogenous,TNFSF13,NM_003808.3,55
287       Endogenous,CLECL1,NM_172004.3,18
288    Endogenous,TNFRSF10B,NM_003842.3,59
289       Endogenous,MAGEC2,NM_016249.3,16
290       Endogenous,CDKN2A,NM_000077.4,91
291         Endogenous,ADM,NM_001124.2,178
292      Endogenous,PNOC,NM_001284244.1,35
293        Endogenous,CD247,NM_198053.2,39
294        Endogenous,PTPRC,NM_080921.3,61
295        Endogenous,OAS3,NM_006187.3,756
296         Endogenous,LAG3,NM_002286.5,86
297       Endogenous,FOSL1,NM_005438.3,118
298     Endogenous,EOMES,NM_001278182.1,38
299       Endogenous,IL10RA,NM_001558.2,76
300        Endogenous,WDR76,NM_024908.3,70
301         Endogenous,GPC4,NM_001448.2,51
302       Endogenous,SLAMF7,NM_021181.3,35
303      Endogenous,RSAD2,NM_080657.4,1136
304         Endogenous,TLR5,NM_003268.5,88
305   Endogenous,VEGFA,NM_001171623.1,1871
306      Endogenous,COL5A1,NM_000093.4,710
307         Endogenous,CD3D,NM_000732.4,41
308     Endogenous,FBP1,NM_001127628.1,226
309      Endogenous,ERO1A,NM_014584.2,1094
310        Endogenous,CCL21,NM_002989.2,18
311     Endogenous,E2F3,NM_001243076.2,174
312    Endogenous,LDHA,NM_001135239.1,7634
313        Endogenous,MS4A1,NM_021950.3,32
314         Endogenous,CD69,NM_001781.2,45
315     Endogenous,SERPINB5,NM_002639.4,46
316         Endogenous,FAP,NM_004460.2,331
317       Endogenous,ITGA2,NM_002203.3,160
318      Endogenous,SIGLEC5,NM_003830.3,16
319    Endogenous,SIRPB2,NM_001134836.1,21
320    Endogenous,EPM2AIP1,NM_014805.3,333
321        Endogenous,FGF18,NM_003862.2,12
322        Endogenous,HRAS,NM_005343.3,134
323       Endogenous,CCND1,NM_053056.2,823
324        Endogenous,LAMB3,NM_000228.2,63
325          Endogenous,ID4,NM_001546.3,24
326         Endogenous,CCL4,NM_002984.2,53
327         Endogenous,GZMH,NM_033423.3,15
328     Endogenous,API5,NM_001142930.1,525
329       Endogenous,PTGER4,NM_000958.2,32
330        Endogenous,ITGB8,NM_002214.2,39
331        Endogenous,TNKS,NM_003747.2,120
332        Endogenous,B2M,NM_004048.2,8147
333        Endogenous,TP53,NM_000546.2,118
334       Endogenous,MAGEB2,NM_002364.4,16
335         Endogenous,LYZ,NM_000239.2,298
336         Endogenous,NCAM1,NM_000615.6,9
337      Endogenous,TCL1A,NM_001098725.1,6
338           Endogenous,HDC,NM_002112.3,7
339         Endogenous,CD27,NM_001242.4,15
340    Endogenous,SBNO2,NM_001100122.1,181
341      Endogenous,PECAM1,NM_000442.4,251
342 Endogenous,SERPINH1,NM_001207014.1,131
343       Endogenous,SPP1,NM_000582.2,3435
344         Endogenous,EGFR,NM_005228.3,57
345        Endogenous,CASP8,NM_001228.4,35
346     Endogenous,CCNA1,NM_001111045.1,15
347   Endogenous,TNFAIP3,NM_001270508.1,36
348       Endogenous,CDC25C,NM_001790.4,33
349        Endogenous,CXCR6,NM_006564.1,16
350         Endogenous,DLL1,NM_005618.3,13
351    Endogenous,OAS1,NM_001032409.1,1120
352     Endogenous,HLA-DQB1,NM_002123.3,59
353        Endogenous,ROBO4,NM_019055.5,26
354       Endogenous,NFKB1,NM_003998.3,242
355     Endogenous,IFI27,NM_005532.3,11191
356     Endogenous,HLA-DMB,NM_002118.3,104
357       Endogenous,CDKN1C,NM_000076.2,43
358        Endogenous,CEP55,NM_018131.3,70
359         Endogenous,ARG1,NM_000045.3,13
360       Endogenous,PLOD2,NM_182943.2,642
361     Endogenous,LAIR1,NM_001289023.2,36
362         Endogenous,SHC2,NM_012435.2,40
363       Endogenous,STAT3,NM_003150.3,997
364      Endogenous,CD45RO,NM_080921.3,122
365         Endogenous,CD2,NM_001767.3,105
366         Endogenous,IL7R,NM_002185.3,31
367     Endogenous,FLNB,NM_001164319.1,673
368    Endogenous,PSMB5,NM_001130725.1,528
369   Endogenous,SLC1A5,NM_001145144.1,195
370   Endogenous,RICTOR,NM_001285439.1,250
371        Endogenous,ZAP70,NM_001079.3,34
372     Endogenous,TNFAIP6,NM_007115.3,151
373       Endogenous,BTLA,NM_001085357.1,8
374        Endogenous,RELA,NM_021975.3,156
375        Endogenous,MMP7,NM_002423.3,184
376        Endogenous,TCF3,NM_003200.3,201
377         Endogenous,IRF8,NM_002163.2,40
378          Endogenous,NOS2,NM_000625.4,6
379         Endogenous,A2M,NM_000014.4,694
380     Endogenous,CCL20,NM_001130046.1,20
381       Endogenous,MKI67,NM_002417.2,308
382      Endogenous,IFNGR1,NM_000416.2,202
383       Endogenous,INHBA,NM_002192.2,161
384        Endogenous,WNT5B,NM_030775.2,35
385        Endogenous,CXCL5,NM_002994.4,21
386         Endogenous,SOX10,NM_006941.3,8
387        Endogenous,EGR1,NM_001964.2,127
388     Endogenous,STAT4,NM_001243835.1,23
389    Endogenous,IFIT3,NM_001031683.3,490
390      Endogenous,GMIP,NM_001288998.1,12
391       Endogenous,ARNT2,NM_014862.3,153
392       Endogenous,UBE2C,NM_007019.2,188
393        Endogenous,CHUK,NM_001278.4,222
394          Endogenous,GHR,NM_000163.2,64
395       Endogenous,TPI1,NM_000365.5,2927
396       Endogenous,HAVCR2,NM_032782.3,81
397        Endogenous,GOT2,NM_002080.3,505
398      Endogenous,PIK3CA,NM_006218.2,103
399        Endogenous,TNFSF9,NM_003811.3,7
400         Endogenous,IDO1,NM_002164.5,24
401        Endogenous,APOE,NM_000041.2,553
402    Endogenous,LILRB2,NM_001278405.1,27
403       Endogenous,PARP4,NM_006437.3,283
404        Endogenous,PFKM,NM_000289.5,133
405        Endogenous,THY1,NM_006288.3,305
406       Endogenous,SAMD9,NM_017654.3,497
407       Endogenous,TGFB1,NM_000660.4,420
408         Endogenous,CD8A,NM_001768.6,24
409         Endogenous,SELE,NM_000450.2,23
410       Endogenous,CDKN2B,NM_004936.3,77
411       Endogenous,CD5,NM_001346456.1,18
412      Endogenous,HLA-A,NM_002116.7,1921
413         Endogenous,FZD8,NM_031866.1,21
414      Endogenous,BCL2L1,NM_001191.3,231
415      Endogenous,TNFRSF9,NM_001561.5,22
416       Endogenous,XCL1/2,NM_002995.2,37
417    Endogenous,MAGEA4,NM_001011548.1,10
418        Endogenous,PMS2,NM_000535.6,249
419        Endogenous,KLRD1,NM_002262.3,18
420       Endogenous,NFATC2,NM_173091.2,73
421       Endogenous,VEGFB,NM_003377.3,154
422        Endogenous,CDC20,NM_001255.1,52
423      Endogenous,OTOA,NM_001161683.1,11
424    Endogenous,TPSAB1/B2,NM_003294.3,84
425       Endogenous,P4HA1,NM_000917.3,415
426        Endogenous,P2RY13,NM_023914.2,9
427         Endogenous,EXO1,NM_006027.3,37
428          Endogenous,CD70,NM_001252.3,6
429        Endogenous,DDB2,NM_000107.2,166
430     Endogenous,NDUFA4L2,NM_020142.3,26
431     Endogenous,IFITM1,NM_003641.3,3082
432      Endogenous,IFNAR1,NM_000629.2,220
433     Endogenous,TREM1,NM_001242589.2,44
434       Endogenous,CXCL13,NM_006419.2,66
435     Endogenous,TWIST2,NM_001271893.3,6
436    Endogenous,HLA-DRB1,NM_002124.3,572
437    Endogenous,FGFR1,NM_001174064.1,286
438       Endogenous,TBXAS1,NM_001061.4,40
439       Endogenous,NCR1,NM_001145457.2,5
440        Endogenous,SOX11,NM_003108.3,25
441     Endogenous,TLR2,NM_001318787.1,129
442        Endogenous,TWF1,NM_002822.4,541
443         Endogenous,CCL5,NM_002985.2,64
444        Endogenous,ITGAL,NM_002209.2,22
445        Endogenous,MYCT1,NM_025107.2,23
446         Endogenous,CD96,NM_005816.4,13
447     Endogenous,PROM1,NM_001145847.1,20
448        Endogenous,OASL,NM_003733.2,158
449         Endogenous,IFNG,NM_000619.2,11
450        Endogenous,BATF3,NM_018664.2,23
451        Endogenous,EZH2,NM_004456.4,107
452         Endogenous,IRF5,NM_002200.3,34
453     Endogenous,PCK2,NM_001018073.2,137
454       Endogenous,EPCAM,NM_002354.2,498
455         Endogenous,CD19,NM_001770.4,19
456         Endogenous,GBP4,NM_052941.4,93
457         Endogenous,MSH6,NM_000179.2,72
458    Endogenous,TNFRSF11B,NM_002546.3,30
459       Endogenous,NOTCH1,NM_017617.3,54
460     Endogenous,CASP9,XM_011542270.1,40
461       Endogenous,RAD51C,NM_058216.2,45
462     Endogenous,HLA-DMA,NM_006120.3,333
463        Endogenous,SFRP1,NM_003012.3,29
464       Endogenous,MAGEA1,NM_004988.4,23
465   Endogenous,ENTPD1,NM_001098175.1,107
466        Endogenous,ROCK1,NM_005406.2,94
467      Endogenous,FCGR2A,NM_021642.3,184
468         Endogenous,NGFR,NM_002507.3,23
469       Endogenous,ALDOC,NM_005165.2,419
470        Endogenous,CCNE1,NM_001238.1,59
471       Endogenous,ITGAX,NM_000887.4,115
472          Endogenous,BLM,NM_000057.3,60
473        Endogenous,MLANA,NM_005511.1,20
474       Endogenous,FCGR1A,NM_000566.3,49
475        Endogenous,CD47,NM_001777.3,925
476         Endogenous,CSF2,NM_000758.3,13
477         Endogenous,CDH5,NM_001795.3,31
478      Endogenous,SLC7A5,NM_003486.6,316
479      Endogenous,GIMAP4,NM_018326.2,103
480       Endogenous,HIF1A,NM_181054.2,705
481     Endogenous,CDK2,NM_001290230.1,188
482        Endogenous,PDCD1,NM_005018.1,12
483         Endogenous,ATF3,NM_001674.3,66
484         Endogenous,TIE1,NM_005424.4,40
485     Endogenous,CD44,NM_001001392.1,630
486      Endogenous,ALDOA,NM_000034.3,4299
487          Endogenous,FAS,NM_000043.3,35
488    Endogenous,MRE11,NM_001330347.1,156
489         Endogenous,IL10,NM_000572.2,14
490         Endogenous,BMP2,NM_001200.3,10
491         Endogenous,BAX,NM_004324.3,291
492    Endogenous,EIF5AL1,NM_001099692.1,5
493          Endogenous,KIT,NM_000222.2,16
494      Endogenous,CDK6,NM_001145306.1,27
495         Endogenous,SPIB,NM_003121.3,10
496       Endogenous,PFKFB3,NM_004566.3,36
497       Endogenous,CXCL12,NM_199168.3,18
498          Endogenous,CSF3,NM_000759.3,7
499      Endogenous,KIR2DL3,NM_015868.2,17
500         Endogenous,CD40,NM_001250.5,40
501        Endogenous,IRF1,NM_002198.2,223
502        Endogenous,MGMT,NM_002412.3,183
503       Endogenous,GLUD1,NM_005271.2,334
504       Endogenous,IFI35,NM_005533.4,240
505          Endogenous,PF4,NM_002619.3,14
506     Endogenous,GPSM3,NM_001276501.1,39
507       Endogenous,SLC2A1,NM_006516.2,72
508          Endogenous,IL2,NM_000586.2,15
509        Endogenous,SNAI1,NM_005985.3,60
510  Endogenous,CTNNB1,NM_001098209.1,1955
511      Endogenous,NOTCH2,NM_024408.3,351
512    Endogenous,NFKB2,NM_001077494.3,124
513         Endogenous,IL33,NM_033439.3,18
514        Endogenous,TREM2,NM_018965.3,64
515        Endogenous,LAMC2,NM_005562.2,43
516      Endogenous,AQP9,NM_001320635.1,45
517        Endogenous,PRKCA,NM_002737.2,17
518         Endogenous,TSLP,NM_033035.4,15
519       Endogenous,HLA-DOB,NM_002120.3,9
520   Endogenous,ANGPTL4,NM_001039667.2,93
521     Endogenous,TNFRSF25,NM_148970.1,43
522    Endogenous,MS4A4A,NM_001243266.1,84
523       Endogenous,CLEC5A,NM_013252.2,39
524        Endogenous,ITGAM,NM_000632.3,19
525         Endogenous,MMP9,NM_004994.2,57
526          Endogenous,CD7,NM_006137.6,14
527          Endogenous,VHL,NM_198156.1,70
528      Endogenous,OLFML2B,NM_015441.1,45
529          Endogenous,IL6,NM_000600.3,24
530    Endogenous,TNFRSF1A,NM_001065.2,330
531         Endogenous,DKK1,NM_012242.2,14
532     Endogenous,FANCA,NM_001018112.1,38
533          Endogenous,TNF,NM_000594.3,58
534          Endogenous,LTB,NM_002341.1,18
535  Endogenous,PPARGC1B,NM_001172699.1,25
536  Endogenous,RPS6KB1,NM_001272042.1,133
537         Endogenous,CD38,NM_001775.2,24
538       Endogenous,DTX3L,NM_138287.3,598
539     Endogenous,TMEM173,NM_198282.1,279
540        Endogenous,NEIL1,NM_024608.2,66
541    Endogenous,HELLS,NM_001289067.1,168
542   Endogenous,TGFBR1,NM_001130916.2,206
543       Endogenous,MB21D1,NM_138441.2,45
544      Endogenous,CCR2,NM_001123041.2,17
545        Endogenous,MSH2,NM_000251.1,227
546        Endogenous,RAD51,NM_133487.3,26
547     Endogenous,TNFRSF18,NM_148901.1,26
548    Endogenous,FCGR3A/B,NM_000570.4,325
549      Endogenous,STAT1,NM_007315.3,2167
550        Endogenous,CTSS,NM_004079.3,430
551        Endogenous,PDK1,NM_002610.3,435
552    Endogenous,ITGAV,NM_001144999.2,612
553    Endogenous,ANGPT1,NM_001199859.1,21
554        Endogenous,BCL6B,NM_181844.3,15
555         Endogenous,CDH2,NM_001792.3,48
556       Endogenous,CSF3R,NM_000760.3,166
557         Endogenous,RELB,NM_006509.3,82
558   Endogenous,CXCL16,NM_001100812.1,109
559         Endogenous,IL6R,NM_000565.3,27
560        Endogenous,PDGFA,NM_033023.4,35
561   Endogenous,PIK3R1,NM_001242466.1,119
562         Endogenous,HK1,NM_000188.2,499
563          Endogenous,AXL,NM_001699.4,65
564         Endogenous,HK2,NM_000189.4,658
565      Endogenous,PDGFRB,NM_002609.3,347
566         Endogenous,FADD,NM_003824.3,92
567    Endogenous,CD74,NM_001025159.2,2455
568       Endogenous,RIPK2,NM_003821.5,124
569 Endogenous,CD45RB,ENST00000367367.1,45
570          Endogenous,BAD,NM_004322.3,86
571     Endogenous,PKM,NM_001206796.2,5714
572        Endogenous,KLRB1,NM_002258.2,15
573     Endogenous,ADORA2A,NM_000675.5,128
574   Endogenous,IFIT1,NM_001270930.1,1506
575        Endogenous,UBE2T,NM_014176.1,46
576      Endogenous,RPL23,NM_000978.3,3210
577         Endogenous,ARG2,NM_001172.3,32
578   Endogenous,TGFBR2,NM_001024847.2,114
579  Endogenous,CRABP2,NM_001199723.1,2655
580       Endogenous,BLK,NM_001330465.1,18
581        Endogenous,CCL14,NM_032962.4,41
582       Endogenous,CCNB1,NM_031966.2,421
583       Endogenous,STAT2,NM_005419.2,998
584    Endogenous,IKBKB,NM_001190720.2,238
585     Endogenous,ZEB2,NM_001171653.1,214
586       Endogenous,LRRC32,NM_005512.2,85
587      Endogenous,IL22RA1,NM_021258.2,33
588         Endogenous,ELOB,NM_007108.2,42
589        Endogenous,ITGA1,NM_181501.1,70
590      Endogenous,IL24,NM_001185158.1,20
591        Endogenous,PVRIG,NM_024070.3,49
592         Endogenous,RB1,NM_000321.2,252
593    Endogenous,SRP54,NM_001146282.1,170
594        Endogenous,ICAM3,NM_002162.3,90
595         Endogenous,CCR5,NM_000579.3,49
596     Endogenous,CTLA4,NM_001037631.2,25
597          Endogenous,GLS,NM_014905.4,68
598       Endogenous,ITGAE,NM_002208.4,120
599         Endogenous,MET,NM_000245.2,110
600        Endogenous,WNT3A,NM_033131.3,18
601     Endogenous,TYMP,NM_001113755.2,752
602    Endogenous,IFI16,NM_001206567.1,207
603       Endogenous,PVR,NM_001135768.2,68
604    Endogenous,P4HA2,NM_001017973.1,157
605        Endogenous,BRIP1,NM_032043.2,71
606         Endogenous,ESR1,NM_000125.2,23
607     Endogenous,DAB2,NM_001244871.1,120
608       Endogenous,DUSP1,NM_004417.3,111
609         Endogenous,CD8B,NM_172213.2,30
610       Endogenous,ACVR1C,NM_145259.2,29
611         Endogenous,IL15,NM_000585.4,25
612   Endogenous,KIR3DL1,NM_001322168.1,19
613       Endogenous,CDH1,NM_004360.3,3142
614        Endogenous,HES1,NM_005524.2,267
615          Endogenous,IHH,NM_002181.2,18
616        Endogenous,CCL19,NM_006274.2,24
617          Endogenous,C2,NM_000063.5,107
618         Endogenous,TLR7,NM_016562.3,23
619        Endogenous,IL2RA,NM_000417.2,19
620       Endogenous,PRKAA2,NM_006252.3,27
621   Endogenous,COL11A2,NM_001163771.1,13
622    Endogenous,TNFRSF10D,NM_003840.4,22
623      Endogenous,SIGLEC8,NM_014442.2,13
624          Endogenous,PC,NM_000920.3,103
625        Endogenous,IL17A,NM_002190.2,24
626         Endogenous,GLI1,NM_005269.2,19
627      Endogenous,GNG4,NM_001098721.1,37
628     Endogenous,LDHB,NM_001174097.2,572
629         Endogenous,DTX4,NM_015177.1,78
630         Endogenous,CD3G,NM_000073.2,14
631     Endogenous,S100A8,NM_002964.4,2954
632      Endogenous,ZC3H12A,NM_025079.2,29
633        Endogenous,IER3,NM_003897.3,280
634          Endogenous,CD4,NM_000616.4,29
635      Endogenous,S100A12,NM_005621.1,21
636       Endogenous,CD6,NM_001254751.1,16
637       Endogenous,CD163,NM_203416.2,144
638        Endogenous,DUSP2,NM_004418.3,22
639    Endogenous,HERC6,NM_001165136.1,158
640         Endogenous,MRC1,NM_002438.2,23
641         Endogenous,DLL4,NM_019074.2,36
642    Endogenous,SAMSN1,NM_001256370.1,63
643      Endogenous,CD28,NM_001243077.1,19
644        Endogenous,TAP2,NM_018833.2,321
645          Endogenous,ICOS,NM_012092.3,6
646      Endogenous,TNFSF12,NM_003809.2,45
647      Endogenous,IFITM2,NM_006435.2,956
648    Endogenous,DNMT1,NM_001130823.2,319
649       Endogenous,TNFSF8,NM_001244.3,32
650     Endogenous,TGFB2,NM_001135599.3,48
651      Endogenous,TMEM140,NM_018295.3,64
652     Endogenous,COL11A1,NM_001854.3,514
653       Endogenous,GIMAP6,NR_024115.1,20
654         Endogenous,IRF4,NM_002460.1,33
655       Endogenous,BNIP3,NM_004052.3,445
656        Endogenous,FPR3,NM_002030.4,225
657      Endogenous,HLA-C,NM_002117.4,1786
658       Endogenous,VEGFC,NM_005429.4,135
659      Endogenous,SIGLEC1,NM_023068.3,58
660          Endogenous,BID,NM_001196.3,40
661    Endogenous,MAPK10,NM_001318067.1,62
662         Endogenous,FCN1,NM_002003.4,16
663        Endogenous,H2AFX,NM_002105.2,71
664      Endogenous,CBLC,NM_001130852.1,34
665       Endogenous,CASP3,NM_032991.2,224
666       Endogenous,PIAS4,NM_015897.2,200
667    Endogenous,HLA-DRA,NM_019111.3,1430
668        Endogenous,ULBP2,NM_025217.2,19
669        Endogenous,CASP1,NM_001223.4,71
670        Endogenous,MS4A2,NM_000139.3,18
671      Endogenous,HSD11B1,NM_181755.2,21
672         Endogenous,GAS1,NM_002048.2,47
673         Endogenous,FUT4,NM_002033.3,41
674         Endogenous,CSF1,NM_000757.5,59
675       Endogenous,FAM30A,NR_026800.2,23
676    Endogenous,ITPK1,NM_001142593.2,273
677        Endogenous,BCAT1,NM_005504.6,81
678         Endogenous,CD80,NM_005191.3,43
679        Endogenous,C1QB,NM_000491.3,302
680         Endogenous,RELN,NM_005045.3,18
681        Endogenous,ICAM5,NM_003259.3,16
682        Endogenous,MAML2,NM_032427.1,39
683        Endogenous,OLR1,NM_002543.3,107
684       Endogenous,NFKBIE,NM_004556.2,58
685     Endogenous,WNT11,XM_011545241.2,20
686    Endogenous,LILRA3,NM_001172654.2,28
687  Endogenous,TNFSF13B,NM_001145645.2,51
688        Endogenous,TDO2,NM_005651.3,102
689       Endogenous,MAP3K5,NM_005923.3,64
690    Endogenous,HLA-F,NM_001098479.1,303
691         Endogenous,CD3E,NM_000733.3,28
692        Endogenous,RRM2,NM_001034.1,714
693           Endogenous,C7,NM_000587.2,33
694    Endogenous,TNFRSF14,NM_003820.3,203
695       Endogenous,FCGRT,NM_004107.4,216
696         Endogenous,WNT2,NM_003391.2,41
697         Endogenous,MICB,NM_005931.3,40
698       Endogenous,HMGA1,NM_145902.2,253
699        Endogenous,IL21R,NM_021798.3,19
700    Endogenous,CD300A,NM_001256841.1,38
701      Endogenous,TWIST1,NM_000474.3,160
702        Endogenous,IL1RN,NM_000577.3,34
703        Endogenous,CXCL1,NM_001511.3,18
704    Endogenous,SFXN1,NM_001322977.1,662
705         Endogenous,GNLY,NM_012483.3,11
706        Endogenous,NID2,NM_007361.3,231
707     Endogenous,NECTIN1,NM_002855.4,180
708 Endogenous,SERPINA1,NM_001127702.1,164
709        Endogenous,PDGFB,NM_002608.2,45
710      Endogenous,HLA-B,NM_005514.6,4911
711       Endogenous,VCAM1,NM_001078.3,190
712    Endogenous,HLA-DPB1,NM_002121.5,383
713      Endogenous,HLA-DOA,NM_002119.3,29
714        Endogenous,GBP2,NM_004120.4,128
715         Endogenous,ATM,NM_000051.3,343
716       Endogenous,PSMB8,NM_004159.4,275
717        Endogenous,MLH1,NM_000249.2,173
718        Endogenous,PLA1A,NM_015900.2,23
719        Endogenous,NT5E,NM_002526.3,109
720        Endogenous,PALMD,NM_017734.4,23
721        Endogenous,UBA7,NM_003335.2,148
722    Endogenous,PIK3CD,NM_001350234.1,36
723         Endogenous,NOD2,NM_022162.1,36
724   Endogenous,CEACAM3,NM_001277163.2,33
725        Endogenous,RIPK3,NM_006871.3,43
726        Endogenous,IL1R2,NR_048564.1,16
727        Endogenous,JAK1,NM_002227.1,316
728       Endogenous,ENO1,NM_001428.3,5271
729    Endogenous,LILRA1,NM_001278318.1,27
730         Endogenous,BBS1,NM_024649.4,83
731       Endogenous,MYD88,NM_002468.3,214
732     Endogenous,CXCR3,NM_001142797.1,13
733          Endogenous,CD1C,NM_001765.2,9
734         Endogenous,TLR9,NM_017442.2,20
735         Endogenous,CCL7,NM_006273.3,67
736         Endogenous,CPA3,NM_001870.2,68
737    Endogenous,SH2D1A,NM_001114937.2,20
738         Endogenous,CCR4,NM_005508.4,33
739        Endogenous,HDAC4,NM_006037.3,46
740     Endogenous,POLD1,NM_001256849.1,44
741   Endogenous,PTPN11,NM_001330437.1,610
742        Endogenous,JAK2,NM_004972.2,152
743       Endogenous,WNT10A,NM_025216.2,17
744       Endogenous,ITGB2,NM_000211.3,166
745        Endogenous,TYMS,NM_001071.1,269
746       Endogenous,KAT2B,NM_003884.4,125
747     Endogenous,ITGA6,NM_001316306.1,65
748        Endogenous,TBX21,NM_013351.1,24
749        Endogenous,BRCA1,NM_007294.3,42
750      Endogenous,COL17A1,NM_000494.3,51
751        Endogenous,BIRC3,NM_001165.4,20
752        Endogenous,KRAS,NM_004985.3,151
753       Endogenous,IL11RA,NM_147162.1,39
754    Endogenous,SIRPA,NM_001040023.1,101
755       Endogenous,CEBPB,NM_005194.3,357
756    Endogenous,VTCN1,NM_001253849.1,755
757        Endogenous,SGK1,NM_005627.3,161
758       Endogenous,NLRC5,NM_032206.4,135
759        Endogenous,CCL8,NM_005623.2,271
760     Endogenous,TRAF1,NM_001190945.1,25
761      Endogenous,ADAM12,NM_003474.5,523
762        Endogenous,MMRN2,NM_024756.2,61
763        Endogenous,PTGS2,NM_000963.1,29
764       Endogenous,SMAD5,NM_005903.5,224
765          Endogenous,LCK,NM_005356.4,34
766        Endogenous,ITGB3,NM_000212.2,45
767    Endogenous,FCGR2B,NM_001002273.1,99
768        Endogenous,NRAS,NM_002524.4,294
769      Endogenous,IL34,NM_001172771.1,40
770        Endogenous,LAMA1,NM_005559.3,57
771       Endogenous,CLEC4E,NM_014358.3,34
772    Endogenous,IL18R1,NM_001282399.1,40
773         Endogenous,MFNG,NM_002405.3,98
774      Endogenous,TTC30A,NM_152275.3,124
775    Endogenous,TNFRSF10C,NM_003841.3,73
776    Positive,POS_C(8),ERCC_00002.1,3852
777 Positive,POS_A(128),ERCC_00117.1,36727
778  Positive,POS_F(0.125),ERCC_00034.1,75
779     Positive,POS_D(2),ERCC_00092.1,725
780  Positive,POS_B(32),ERCC_00112.1,14523
781   Positive,POS_E(0.5),ERCC_00035.1,150
782      Negative,NEG_C(0),ERCC_00019.1,27
783       Negative,NEG_D(0),ERCC_00076.1,8
784      Negative,NEG_E(0),ERCC_00098.1,24
785      Negative,NEG_A(0),ERCC_00096.1,17
786      Negative,NEG_H(0),ERCC_00154.1,12
787      Negative,NEG_G(0),ERCC_00144.1,14
788      Negative,NEG_F(0),ERCC_00126.1,39
789      Negative,NEG_B(0),ERCC_00041.1,20
790      Housekeeping,UBB,NM_018955.3,3440
791   Housekeeping,PUM1,NM_001020658.1,615
792      Housekeeping,TLK2,NM_006852.3,144
793   Housekeeping,DNAJC14,NM_032364.5,201
794     Housekeeping,SF3A1,NM_005877.4,315
795    Housekeeping,POLR2A,NM_000937.2,460
796      Housekeeping,SDHA,NM_004168.3,339
797   Housekeeping,STK11IP,NM_052902.2,103
798     Housekeeping,NRDE2,NM_017970.3,179
799    Housekeeping,TBP,NM_001172085.1,117
800     Housekeeping,OAZ1,NM_004152.2,2242
801   Housekeeping,TBC1D10B,NM_015527.3,92
802      Housekeeping,GUSB,NM_000181.1,146
803     Housekeeping,PSMC4,NM_006503.2,209
804      Housekeeping,TFRC,NM_003234.1,489
805     Housekeeping,ABCF1,NM_001090.2,170
806      Housekeeping,TMUB2,NM_177441.2,82
807    Housekeeping,MRPL19,NM_014763.3,232
808       Housekeeping,G6PD,NM_000402.4,92
809     Housekeeping,ERCC3,NM_000122.1,454
810                        </Code_Summary>
811                             <Messages>
812                            </Messages>
# Cleaned cobined pre and post data for 5 patients
read.csv(here("data/02_dat_clean.csv"))
      code_class         gene   accesion_number pre_count_1 post_count_1
1     Endogenous         CCNO       NM_021147.4          14           14
2     Endogenous          MYC       NM_002467.3         632          427
3     Endogenous        CD79A       NM_001783.3          10           17
4     Endogenous        FSTL3       NM_005860.2          45           59
5     Endogenous         VCAN    NM_001126336.2        1141          838
6     Endogenous       CX3CL1       NM_002996.3          59           57
7     Endogenous        ERBB2       NM_004448.2         315          807
8     Endogenous      FAM124B    NM_001122779.1          21           23
9     Endogenous         AKT1       NM_005163.2        1050         1259
10    Endogenous          KDR       NM_002253.2          79          152
11    Endogenous          EGF    NM_001178130.2          78            8
12    Endogenous      MAGEA12    NM_001166386.1         125            7
13    Endogenous        IFNA1       NM_024013.1          65           27
14    Endogenous        TGFB3    NM_001329938.1          75          130
15    Endogenous        MFGE8    NM_001114614.1         528          494
16    Endogenous        CXCL2       NM_002089.1          87           18
17    Endogenous        CCND2       NM_001759.2         144          226
18    Endogenous     PDZK1IP1       NM_005764.3          27           17
19    Endogenous         JAG2       NM_002226.4          38           30
20    Endogenous           C5    NM_001317163.1          21           74
21    Endogenous        CD79B    NM_001039933.1          13           11
22    Endogenous        CXCR2       NM_001557.3          17           23
23    Endogenous       PSMB10       NM_002801.3          79           77
24    Endogenous         ZEB1    NM_001128128.2         138          219
25    Endogenous         ANLN       NM_018685.2         121           22
26    Endogenous         TAF3       NM_031923.3          19           22
27    Endogenous        CD276    NM_001024736.1         939          482
28    Endogenous        ICAM1       NM_000201.2          70           29
29    Endogenous         IL16       NM_004513.4          52           67
30    Endogenous        CXCL3       NM_002090.2          17           10
31    Endogenous         PRR5       NM_015366.3          48           36
32    Endogenous         CTSW       NM_001335.3          13           14
33    Endogenous        CXCR4    NM_001008540.1         298          147
34    Endogenous       IFNGR2       NM_005534.3         483          326
35    Endogenous        CDH11       NM_001797.2         725          735
36    Endogenous       COL6A3       NM_004369.3        1878         1155
37    Endogenous         GZMK       NM_002104.2          17           12
38    Endogenous         IRF2       NM_002199.3         165          184
39    Endogenous        RPL7A       NM_000972.2        2589         4987
40    Endogenous       GPR160       NM_014373.1         198          678
41    Endogenous         MICA       NM_000247.1          52           41
42    Endogenous       TAPBPL       NM_018009.4          88          132
43    Endogenous       CXCL14       NM_004887.4         167         6855
44    Endogenous         CD14    NM_001174105.1          88          213
45    Endogenous         IL18    NM_001243211.1          65           34
46    Endogenous      CLEC14A       NM_175060.1          24           95
47    Endogenous        HMGB1       NM_002128.5         102          140
48    Endogenous        KIF2C       NM_006845.2          64           23
49    Endogenous         RNLS    NM_001031709.2          35           69
50    Endogenous        RPTOR    NM_001163034.1         126           99
51    Endogenous         CD68       NM_001251.2         109           66
52    Endogenous        CCL13       NM_005408.2           9           16
53    Endogenous         CYBB       NM_000397.3         169          243
54    Endogenous      PLA2G2A       NM_000300.2          16           31
55    Endogenous        FGF13    NM_001139498.1          22           46
56    Endogenous        CNTFR       NM_147164.2          15           22
57    Endogenous        CD244    NM_001166663.1          17           11
58    Endogenous       CSF2RB       NM_000395.2          17           24
59    Endogenous       MAP3K7       NM_003188.3         278          389
60    Endogenous        FASLG       NM_000639.2          16           14
61    Endogenous        CD209       NM_021155.2          13           32
62    Endogenous         IRF7       NM_004029.2         465          177
63    Endogenous        PTCD2    NM_001284403.1         117          174
64    Endogenous       PIK3R2       NM_005027.3         382          256
65    Endogenous       LILRA5       NM_181879.2          23           17
66    Endogenous         IL32       NM_004221.4         297          165
67    Endogenous        CCND3    NM_001136017.2          45           83
68    Endogenous        BIRC5       NM_001168.2         198           24
69    Endogenous       LGALS9       NM_002308.3          42           41
70    Endogenous       RASAL1    NM_001193520.1          39           28
71    Endogenous     PDCD1LG2       NM_025239.3          39           33
72    Endogenous         IL11       NM_000641.3          51           18
73    Endogenous         PRKX       NM_005044.4          19           13
74    Endogenous         SNCA    NM_001146055.1          16           19
75    Endogenous       ADGRE1    NM_001256252.1          16            9
76    Endogenous        PSMB9       NM_002800.4         115           73
77    Endogenous        RUNX3    NM_001031680.2          26           38
78    Endogenous       PGPEP1    NM_001300927.1          33           60
79    Endogenous         MELK       NM_014791.2         160           53
80    Endogenous        ISG15       NM_005101.3        1631          150
81    Endogenous       EIF2B4    NM_001034116.1         117          104
82    Endogenous         IRF9       NM_006084.4         548          421
83    Endogenous         IL1A       NM_000575.3          32           22
84    Endogenous        FCRL2    NM_001159488.1          13           20
85    Endogenous     EIF4EBP1       NM_004095.3        1412          128
86    Endogenous        LTBP1       NM_000627.3         160           99
87    Endogenous       CD40LG       NM_000074.2           9           13
88    Endogenous         HEY1    NM_001040708.1         166          367
89    Endogenous     HLA-DQA1       NM_002122.3         295           15
90    Endogenous         PRLR       NM_000949.5         601         1434
91    Endogenous    TNFRSF11A    NM_001270949.1          40           20
92    Endogenous         AREG       NM_001657.3          57           46
93    Endogenous         BBC3       NM_014417.4         180          210
94    Endogenous         EDN1       NM_001955.2          36           23
95    Endogenous       PARP12       NM_022750.3         264          130
96    Endogenous       PIK3CG    NM_001282426.1          38           53
97    Endogenous          IL4       NM_172348.1          13           11
98    Endogenous        F2RL1       NM_005242.4          48           19
99    Endogenous        CXCL6       NM_002993.3          20           17
100   Endogenous      TNFSF18       NM_005092.3          17           14
101   Endogenous         JAK3       NM_000215.2          44           23
102   Endogenous         NKG7       NM_005601.3          33           58
103   Endogenous        TAPBP       NM_003190.4         533          546
104   Endogenous         MTOR       NM_004958.3         200          183
105   Endogenous         SELP       NM_003005.3          13           22
106   Endogenous        HLA-E       NM_005516.5         670          644
107   Endogenous         GOT1       NM_002079.2         265          228
108   Endogenous        SMAP1    NM_001044305.2         157          219
109   Endogenous       CDKN1A       NM_000389.2         430          216
110   Endogenous       CD45RA       NM_002838.4           8           20
111   Endogenous        HNF1A       NM_000545.6          12           21
112   Endogenous       TICAM1       NM_182919.3          36           31
113   Endogenous         C1QA       NM_015991.3         100           79
114   Endogenous         CD86    NM_001206924.1          25           19
115   Endogenous        ITGA4       NM_000885.5         108           76
116   Endogenous         ROR2    NM_001318204.1         129           62
117   Endogenous        WNT7B       NM_058238.2          97           12
118   Endogenous         FLT1       NM_002019.4         381          429
119   Endogenous       CTAG1B       NM_001327.2          58           13
120   Endogenous       CLEC7A       NM_197954.2          83           96
121   Endogenous      TNFRSF4       NM_003327.3          18           22
122   Endogenous       MS4A6A       NM_152852.2          27           44
123   Endogenous       ANGPT2       NM_001147.2         113           79
124   Endogenous        APH1B    NM_001145646.1         169          234
125   Endogenous         RORC    NM_001001523.1          56           67
126   Endogenous      NECTIN2    NM_001042724.1         286          578
127   Endogenous         DPP4       NM_001935.3          31           23
128   Endogenous         CCL2       NM_002982.3         789          150
129   Endogenous          NF1       NM_000267.3         168          178
130   Endogenous       S100A9       NM_002965.3        1519           32
131   Endogenous       NFKBIA       NM_020529.2        1304          903
132   Endogenous       BNIP3L    NM_001330491.1         267          102
133   Endogenous         CST2       NM_001322.2          24           44
134   Endogenous        APOL6       NM_030641.3         178          140
135   Endogenous         BRD4    NM_001330384.1         320          191
136   Endogenous      SLC16A1       NM_003051.3         264           72
137   Endogenous         THBD       NM_000361.2          35           56
138   Endogenous        TIGIT       NM_173799.2          15           14
139   Endogenous         VSIR       NM_022153.1          17           26
140   Endogenous       TRIM21       NM_003141.3         118           62
141   Endogenous          NBN       NM_002485.4         371          151
142   Endogenous         WNT4       NM_030761.4          15           33
143   Endogenous        CXCL8       NM_000584.3          54           12
144   Endogenous         FGF9       NM_002010.2          11           14
145   Endogenous        C5AR1       NM_001736.3          17           17
146   Endogenous     TNFRSF1B       NM_001066.2          25           40
147   Endogenous     HLA-DRB5       NM_002125.3          17         1866
148   Endogenous         GLUL       NM_002065.6        1920         6088
149   Endogenous          LY9    NM_001033667.2           7           16
150   Endogenous         TAP1       NM_000593.5         295          124
151   Endogenous        IFIH1       NM_022168.3         778          225
152   Endogenous       DEPTOR    NM_001283012.1         138          160
153   Endogenous        CSF1R       NM_005211.3         186          275
154   Endogenous        MARCO       NM_006770.3          21           17
155   Endogenous        NFIL3    NM_001289999.1         133           83
156   Endogenous        IKBKG    NM_001099856.4          46           65
157   Endogenous         CD58    NM_001144822.1          36           39
158   Endogenous        LOXL2       NM_002318.2          64           41
159   Endogenous        SPRY4       NM_030964.3          42           81
160   Endogenous        NFAM1       NM_145912.5           9           13
161   Endogenous          SYK       NM_003177.5          61           53
162   Endogenous         COMP       NM_000095.2         314          247
163   Endogenous         IFI6       NM_002038.3       24292         1707
164   Endogenous      RASGRF1    NM_001145648.1         329           15
165   Endogenous        HDAC5    NM_001015053.1         101          216
166   Endogenous        BAMBI       NM_012342.2          43          220
167   Endogenous       MAGEC1       NM_005462.4          12           18
168   Endogenous          FYN       NM_002037.5          89          150
169   Endogenous       TNFSF4    NM_001297562.1          40           26
170   Endogenous        CD274       NM_014143.3          31           15
171   Endogenous       PRKACB       NM_182948.2          47           81
172   Endogenous        IFIT2       NM_001547.4         164           31
173   Endogenous        PPARG       NM_005037.5          31           85
174   Endogenous         PTEN       NM_000314.6         178          244
175   Endogenous        FOXP3       NM_014009.3          20           25
176   Endogenous       SREBF1    NM_001005291.1         870        10672
177   Endogenous         CD36    NM_001001548.2          99          494
178   Endogenous        AXIN1       NM_181050.1          83           74
179   Endogenous        KLRK1       NM_007360.3          19           19
180   Endogenous         GBP1       NM_002053.2         108           22
181   Endogenous       CXCL11       NM_005409.4         175           16
182   Endogenous       CXCL10       NM_001565.3         770           51
183   Endogenous        RIPK1       NM_003804.3         157          346
184   Endogenous          REN       NM_000537.3           6           13
185   Endogenous         PRF1    NM_001083116.1          17           17
186   Endogenous      EIF2AK2    NM_001135652.2         997          545
187   Endogenous          LIF       NM_002309.4          43           21
188   Endogenous         BRD3       NM_007371.3         225          295
189   Endogenous        IGF2R       NM_000876.2         133          315
190   Endogenous         FPR1       NM_002029.3          26           34
191   Endogenous        DUSP5       NM_004419.3        1036          402
192   Endogenous          APC    NM_001127510.2         394          595
193   Endogenous        HDAC3       NM_003883.3         224          400
194   Endogenous         CES3    NM_001185176.1          55           13
195   Endogenous         OAS2       NM_016817.2        1380          173
196   Endogenous       HDAC11    NM_001330636.1          51           86
197   Endogenous        THBS1       NM_003246.2        1778         1329
198   Endogenous      SLC11A1       NM_000578.3          41           21
199   Endogenous    MAGEA3/A6       NM_005362.3         470           10
200   Endogenous       ARID1A       NM_006015.4         316          291
201   Endogenous         CD48       NM_001778.3          26           11
202   Endogenous         GZMA       NM_006144.3          13           19
203   Endogenous       ICOSLG       NM_015259.4         130           92
204   Endogenous       PIK3R5       NM_014308.3          37           39
205   Endogenous         GZMM       NM_005317.2          13           14
206   Endogenous        WNT5A       NM_003392.3         109           25
207   Endogenous         TLR4       NR_024168.1          79          103
208   Endogenous         GZMB       NM_004131.4           8            5
209   Endogenous        PARP9    NM_001146103.1         445          176
210   Endogenous         LY96    NM_001195797.1         154          147
211   Endogenous        RAD50       NM_005732.3         612         1386
212   Endogenous          MX1    NM_001144925.2         451          127
213   Endogenous        CENPF       NM_016343.3         126           11
214   Endogenous         SELL       NM_000655.4           9           24
215   Endogenous      TNFSF10       NM_003810.3         378          277
216   Endogenous      IL12RB2    NM_001319233.1          23           10
217   Endogenous        CXCL9       NM_002416.2          22           26
218   Endogenous        TRAT1       NM_016388.3           5           13
219   Endogenous         STC1       NM_003155.2          61          129
220   Endogenous        IL2RB       NM_000878.2          18           19
221   Endogenous       LILRB4    NM_001278426.3          44           69
222   Endogenous         SOX2       NM_003106.2           9           12
223   Endogenous          HCK    NM_001172129.1          55           59
224   Endogenous        WNT2B    NM_001291880.1          20           43
225   Endogenous         IL1B       NM_000576.2          19           15
226   Endogenous         TLR1       NM_003263.3          60           53
227   Endogenous        CCL22       NM_002990.3          15           11
228   Endogenous        ICAM2       NM_000873.3          19           36
229   Endogenous      MAP3K12       NM_006301.3          59           76
230   Endogenous         JAG1       NM_000214.2         119          178
231   Endogenous      CCL3/L1       NM_021006.5         122           19
232   Endogenous        SOCS1       NM_003745.1          39           12
233   Endogenous         BCL2       NM_000633.2         198          472
234   Endogenous       MAP3K8    NM_001244134.1         213           69
235   Endogenous         MMP1       NM_002421.2          47           24
236   Endogenous       CMKLR1       NM_004072.2          40          118
237   Endogenous     TNFRSF17       NM_001192.2          10           18
238   Endogenous         TLR8       NM_138636.4          21           26
239   Endogenous         TPM1       NM_000366.5         580          406
240   Endogenous      CXorf36       NM_024689.2          48          141
241   Endogenous        NLRP3    NM_001079821.2          16           17
242   Endogenous      DEFB134    NM_001302695.1          16           23
243   Endogenous     HLA-DQA2       NM_020056.4          25           25
244   Endogenous       CX3CR1    NM_001171171.1          11           82
245   Endogenous        APLNR       NM_005161.4           7           41
246   Endogenous         MXI1    NM_001008541.1          88           73
247   Endogenous         FZD9       NM_003508.2          16           15
248   Endogenous       COL4A5       NM_000495.4         101          354
249   Endogenous         FCAR       NM_133278.2          13           11
250   Endogenous        BRCA2       NM_000059.3          85           78
251   Endogenous        SFRP4       NM_003014.2         163          447
252   Endogenous         TLR3       NM_003265.2          89           43
253   Endogenous        IL2RG       NM_000206.1          21           22
254   Endogenous         CD84    NM_001184879.1          60           87
255   Endogenous     HLA-DPA1       NM_033554.2         330          591
256   Endogenous         RBL2    NM_001323611.1         427         1334
257   Endogenous        CCL18       NM_002988.3         135          170
258   Endogenous         IRF3    NM_001197122.1         126          104
259   Endogenous      TNFRSF8       NM_001243.3           4            9
260   Endogenous      KIR3DL2       NM_006737.2           5            7
261   Endogenous      TNFSF13       NM_003808.3          55           52
262   Endogenous       CLECL1       NM_172004.3          18           27
263   Endogenous    TNFRSF10B       NM_003842.3          59           30
264   Endogenous       MAGEC2       NM_016249.3          16           14
265   Endogenous       CDKN2A       NM_000077.4          91          131
266   Endogenous          ADM       NM_001124.2         178           75
267   Endogenous         PNOC    NM_001284244.1          35           37
268   Endogenous        CD247       NM_198053.2          39           40
269   Endogenous        PTPRC       NM_080921.3          61           48
270   Endogenous         OAS3       NM_006187.3         756          156
271   Endogenous         LAG3       NM_002286.5          86           58
272   Endogenous        FOSL1       NM_005438.3         118          108
273   Endogenous        EOMES    NM_001278182.1          38           32
274   Endogenous       IL10RA       NM_001558.2          76           64
275   Endogenous        WDR76       NM_024908.3          70           89
276   Endogenous         GPC4       NM_001448.2          51           41
277   Endogenous       SLAMF7       NM_021181.3          35           56
278   Endogenous        RSAD2       NM_080657.4        1136          147
279   Endogenous         TLR5       NM_003268.5          88           74
280   Endogenous        VEGFA    NM_001171623.1        1871          269
281   Endogenous       COL5A1       NM_000093.4         710          331
282   Endogenous         CD3D       NM_000732.4          41           59
283   Endogenous         FBP1    NM_001127628.1         226          779
284   Endogenous        ERO1A       NM_014584.2        1094          736
285   Endogenous        CCL21       NM_002989.2          18           33
286   Endogenous         E2F3    NM_001243076.2         174          130
287   Endogenous         LDHA    NM_001135239.1        7634          526
288   Endogenous        MS4A1       NM_021950.3          32           67
289   Endogenous         CD69       NM_001781.2          45           47
290   Endogenous     SERPINB5       NM_002639.4          46           33
291   Endogenous          FAP       NM_004460.2         331          136
292   Endogenous        ITGA2       NM_002203.3         160           21
293   Endogenous      SIGLEC5       NM_003830.3          16           22
294   Endogenous       SIRPB2    NM_001134836.1          21           21
295   Endogenous     EPM2AIP1       NM_014805.3         333          166
296   Endogenous        FGF18       NM_003862.2          12           19
297   Endogenous         HRAS       NM_005343.3         134          201
298   Endogenous        CCND1       NM_053056.2         823         2876
299   Endogenous        LAMB3       NM_000228.2          63           43
300   Endogenous          ID4       NM_001546.3          24           52
301   Endogenous         CCL4       NM_002984.2          53           48
302   Endogenous         GZMH       NM_033423.3          15           14
303   Endogenous         API5    NM_001142930.1         525          456
304   Endogenous       PTGER4       NM_000958.2          32           42
305   Endogenous        ITGB8       NM_002214.2          39          247
306   Endogenous         TNKS       NM_003747.2         120          166
307   Endogenous          B2M       NM_004048.2        8147         3820
308   Endogenous         TP53       NM_000546.2         118          102
309   Endogenous       MAGEB2       NM_002364.4          16           10
310   Endogenous          LYZ       NM_000239.2         298          420
311   Endogenous        NCAM1       NM_000615.6           9           83
312   Endogenous        TCL1A    NM_001098725.1           6            4
313   Endogenous          HDC       NM_002112.3           7           23
314   Endogenous         CD27       NM_001242.4          15           30
315   Endogenous        SBNO2    NM_001100122.1         181          146
316   Endogenous       PECAM1       NM_000442.4         251          571
317   Endogenous     SERPINH1    NM_001207014.1         131           58
318   Endogenous         SPP1       NM_000582.2        3435          448
319   Endogenous         EGFR       NM_005228.3          57           50
320   Endogenous        CASP8       NM_001228.4          35           24
321   Endogenous        CCNA1    NM_001111045.1          15           11
322   Endogenous      TNFAIP3    NM_001270508.1          36           18
323   Endogenous       CDC25C       NM_001790.4          33           17
324   Endogenous        CXCR6       NM_006564.1          16           20
325   Endogenous         DLL1       NM_005618.3          13           29
326   Endogenous         OAS1    NM_001032409.1        1120          150
327   Endogenous     HLA-DQB1       NM_002123.3          59            7
328   Endogenous        ROBO4       NM_019055.5          26           52
329   Endogenous        NFKB1       NM_003998.3         242          126
330   Endogenous        IFI27       NM_005532.3       11191         2564
331   Endogenous      HLA-DMB       NM_002118.3         104          176
332   Endogenous       CDKN1C       NM_000076.2          43          224
333   Endogenous        CEP55       NM_018131.3          70            9
334   Endogenous         ARG1       NM_000045.3          13           16
335   Endogenous        PLOD2       NM_182943.2         642          217
336   Endogenous        LAIR1    NM_001289023.2          36           43
337   Endogenous         SHC2       NM_012435.2          40          159
338   Endogenous        STAT3       NM_003150.3         997          849
339   Endogenous       CD45RO       NM_080921.3         122           77
340   Endogenous          CD2       NM_001767.3         105           68
341   Endogenous         IL7R       NM_002185.3          31           16
342   Endogenous         FLNB    NM_001164319.1         673         1468
343   Endogenous        PSMB5    NM_001130725.1         528          445
344   Endogenous       SLC1A5    NM_001145144.1         195          749
345   Endogenous       RICTOR    NM_001285439.1         250         1094
346   Endogenous        ZAP70       NM_001079.3          34           25
347   Endogenous      TNFAIP6       NM_007115.3         151           57
348   Endogenous         BTLA    NM_001085357.1           8           14
349   Endogenous         RELA       NM_021975.3         156          123
350   Endogenous         MMP7       NM_002423.3         184           13
351   Endogenous         TCF3       NM_003200.3         201          105
352   Endogenous         IRF8       NM_002163.2          40           34
353   Endogenous         NOS2       NM_000625.4           6           10
354   Endogenous          A2M       NM_000014.4         694         1423
355   Endogenous        CCL20    NM_001130046.1          20            8
356   Endogenous        MKI67       NM_002417.2         308           30
357   Endogenous       IFNGR1       NM_000416.2         202          440
358   Endogenous        INHBA       NM_002192.2         161           80
359   Endogenous        WNT5B       NM_030775.2          35           17
360   Endogenous        CXCL5       NM_002994.4          21           19
361   Endogenous        SOX10       NM_006941.3           8            9
362   Endogenous         EGR1       NM_001964.2         127          162
363   Endogenous        STAT4    NM_001243835.1          23           34
364   Endogenous        IFIT3    NM_001031683.3         490           67
365   Endogenous         GMIP    NM_001288998.1          12           18
366   Endogenous        ARNT2       NM_014862.3         153          157
367   Endogenous        UBE2C       NM_007019.2         188           13
368   Endogenous         CHUK       NM_001278.4         222          211
369   Endogenous          GHR       NM_000163.2          64          140
370   Endogenous         TPI1       NM_000365.5        2927         1072
371   Endogenous       HAVCR2       NM_032782.3          81           52
372   Endogenous         GOT2       NM_002080.3         505          733
373   Endogenous       PIK3CA       NM_006218.2         103          176
374   Endogenous       TNFSF9       NM_003811.3           7           16
375   Endogenous         IDO1       NM_002164.5          24           17
376   Endogenous         APOE       NM_000041.2         553          284
377   Endogenous       LILRB2    NM_001278405.1          27           29
378   Endogenous        PARP4       NM_006437.3         283          183
379   Endogenous         PFKM       NM_000289.5         133          172
380   Endogenous         THY1       NM_006288.3         305          265
381   Endogenous        SAMD9       NM_017654.3         497           88
382   Endogenous        TGFB1       NM_000660.4         420          421
383   Endogenous         CD8A       NM_001768.6          24           35
384   Endogenous         SELE       NM_000450.2          23           18
385   Endogenous       CDKN2B       NM_004936.3          77          101
386   Endogenous          CD5    NM_001346456.1          18           24
387   Endogenous        HLA-A       NM_002116.7        1921          529
388   Endogenous         FZD8       NM_031866.1          21          462
389   Endogenous       BCL2L1       NM_001191.3         231          333
390   Endogenous      TNFRSF9       NM_001561.5          22            9
391   Endogenous       XCL1/2       NM_002995.2          37           13
392   Endogenous       MAGEA4    NM_001011548.1          10           12
393   Endogenous         PMS2       NM_000535.6         249          281
394   Endogenous        KLRD1       NM_002262.3          18           15
395   Endogenous       NFATC2       NM_173091.2          73           81
396   Endogenous        VEGFB       NM_003377.3         154           98
397   Endogenous        CDC20       NM_001255.1          52           16
398   Endogenous         OTOA    NM_001161683.1          11           16
399   Endogenous    TPSAB1/B2       NM_003294.3          84          148
400   Endogenous        P4HA1       NM_000917.3         415           73
401   Endogenous       P2RY13       NM_023914.2           9           33
402   Endogenous         EXO1       NM_006027.3          37           20
403   Endogenous         CD70       NM_001252.3           6           20
404   Endogenous         DDB2       NM_000107.2         166          137
405   Endogenous     NDUFA4L2       NM_020142.3          26           45
406   Endogenous       IFITM1       NM_003641.3        3082          426
407   Endogenous       IFNAR1       NM_000629.2         220          378
408   Endogenous        TREM1    NM_001242589.2          44           13
409   Endogenous       CXCL13       NM_006419.2          66           54
410   Endogenous       TWIST2    NM_001271893.3           6            9
411   Endogenous     HLA-DRB1       NM_002124.3         572          309
412   Endogenous        FGFR1    NM_001174064.1         286          248
413   Endogenous       TBXAS1       NM_001061.4          40          121
414   Endogenous         NCR1    NM_001145457.2           5            9
415   Endogenous        SOX11       NM_003108.3          25           17
416   Endogenous         TLR2    NM_001318787.1         129           82
417   Endogenous         TWF1       NM_002822.4         541          753
418   Endogenous         CCL5       NM_002985.2          64           47
419   Endogenous        ITGAL       NM_002209.2          22           89
420   Endogenous        MYCT1       NM_025107.2          23           36
421   Endogenous         CD96       NM_005816.4          13           17
422   Endogenous        PROM1    NM_001145847.1          20           12
423   Endogenous         OASL       NM_003733.2         158           15
424   Endogenous         IFNG       NM_000619.2          11           14
425   Endogenous        BATF3       NM_018664.2          23           18
426   Endogenous         EZH2       NM_004456.4         107           27
427   Endogenous         IRF5       NM_002200.3          34           24
428   Endogenous         PCK2    NM_001018073.2         137          184
429   Endogenous        EPCAM       NM_002354.2         498          438
430   Endogenous         CD19       NM_001770.4          19           32
431   Endogenous         GBP4       NM_052941.4          93           77
432   Endogenous         MSH6       NM_000179.2          72           76
433   Endogenous    TNFRSF11B       NM_002546.3          30           26
434   Endogenous       NOTCH1       NM_017617.3          54           71
435   Endogenous        CASP9    XM_011542270.1          40           43
436   Endogenous       RAD51C       NM_058216.2          45          125
437   Endogenous      HLA-DMA       NM_006120.3         333          350
438   Endogenous        SFRP1       NM_003012.3          29           78
439   Endogenous       MAGEA1       NM_004988.4          23           14
440   Endogenous       ENTPD1    NM_001098175.1         107          195
441   Endogenous        ROCK1       NM_005406.2          94          135
442   Endogenous       FCGR2A       NM_021642.3         184          288
443   Endogenous         NGFR       NM_002507.3          23           44
444   Endogenous        ALDOC       NM_005165.2         419          473
445   Endogenous        CCNE1       NM_001238.1          59           22
446   Endogenous        ITGAX       NM_000887.4         115          104
447   Endogenous          BLM       NM_000057.3          60           52
448   Endogenous        MLANA       NM_005511.1          20           18
449   Endogenous       FCGR1A       NM_000566.3          49           81
450   Endogenous         CD47       NM_001777.3         925          409
451   Endogenous         CSF2       NM_000758.3          13           19
452   Endogenous         CDH5       NM_001795.3          31           85
453   Endogenous       SLC7A5       NM_003486.6         316          174
454   Endogenous       GIMAP4       NM_018326.2         103          177
455   Endogenous        HIF1A       NM_181054.2         705          384
456   Endogenous         CDK2    NM_001290230.1         188           98
457   Endogenous        PDCD1       NM_005018.1          12           14
458   Endogenous         ATF3       NM_001674.3          66           31
459   Endogenous         TIE1       NM_005424.4          40           81
460   Endogenous         CD44    NM_001001392.1         630          188
461   Endogenous        ALDOA       NM_000034.3        4299         4732
462   Endogenous          FAS       NM_000043.3          35           14
463   Endogenous        MRE11    NM_001330347.1         156          188
464   Endogenous         IL10       NM_000572.2          14           12
465   Endogenous         BMP2       NM_001200.3          10          240
466   Endogenous          BAX       NM_004324.3         291          159
467   Endogenous      EIF5AL1    NM_001099692.1           5           14
468   Endogenous          KIT       NM_000222.2          16           36
469   Endogenous         CDK6    NM_001145306.1          27           35
470   Endogenous         SPIB       NM_003121.3          10           10
471   Endogenous       PFKFB3       NM_004566.3          36           33
472   Endogenous       CXCL12       NM_199168.3          18           59
473   Endogenous         CSF3       NM_000759.3           7           10
474   Endogenous      KIR2DL3       NM_015868.2          17           22
475   Endogenous         CD40       NM_001250.5          40           67
476   Endogenous         IRF1       NM_002198.2         223          158
477   Endogenous         MGMT       NM_002412.3         183          299
478   Endogenous        GLUD1       NM_005271.2         334          648
479   Endogenous        IFI35       NM_005533.4         240          192
480   Endogenous          PF4       NM_002619.3          14           22
481   Endogenous        GPSM3    NM_001276501.1          39           69
482   Endogenous       SLC2A1       NM_006516.2          72           42
483   Endogenous          IL2       NM_000586.2          15           21
484   Endogenous        SNAI1       NM_005985.3          60           62
485   Endogenous       CTNNB1    NM_001098209.1        1955         1539
486   Endogenous       NOTCH2       NM_024408.3         351          206
487   Endogenous        NFKB2    NM_001077494.3         124           77
488   Endogenous         IL33       NM_033439.3          18           53
489   Endogenous        TREM2       NM_018965.3          64           98
490   Endogenous        LAMC2       NM_005562.2          43           30
491   Endogenous         AQP9    NM_001320635.1          45           24
492   Endogenous        PRKCA       NM_002737.2          17           30
493   Endogenous         TSLP       NM_033035.4          15           17
494   Endogenous      HLA-DOB       NM_002120.3           9           33
495   Endogenous      ANGPTL4    NM_001039667.2          93           10
496   Endogenous     TNFRSF25       NM_148970.1          43           94
497   Endogenous       MS4A4A    NM_001243266.1          84          124
498   Endogenous       CLEC5A       NM_013252.2          39           29
499   Endogenous        ITGAM       NM_000632.3          19           15
500   Endogenous         MMP9       NM_004994.2          57           77
501   Endogenous          CD7       NM_006137.6          14           16
502   Endogenous          VHL       NM_198156.1          70           73
503   Endogenous      OLFML2B       NM_015441.1          45           59
504   Endogenous          IL6       NM_000600.3          24           21
505   Endogenous     TNFRSF1A       NM_001065.2         330          342
506   Endogenous         DKK1       NM_012242.2          14           12
507   Endogenous        FANCA    NM_001018112.1          38           25
508   Endogenous          TNF       NM_000594.3          58           38
509   Endogenous          LTB       NM_002341.1          18           23
510   Endogenous     PPARGC1B    NM_001172699.1          25           41
511   Endogenous      RPS6KB1    NM_001272042.1         133          819
512   Endogenous         CD38       NM_001775.2          24           20
513   Endogenous        DTX3L       NM_138287.3         598          351
514   Endogenous      TMEM173       NM_198282.1         279          227
515   Endogenous        NEIL1       NM_024608.2          66           51
516   Endogenous        HELLS    NM_001289067.1         168           65
517   Endogenous       TGFBR1    NM_001130916.2         206          386
518   Endogenous       MB21D1       NM_138441.2          45           84
519   Endogenous         CCR2    NM_001123041.2          17           12
520   Endogenous         MSH2       NM_000251.1         227          193
521   Endogenous        RAD51       NM_133487.3          26            9
522   Endogenous     TNFRSF18       NM_148901.1          26           23
523   Endogenous     FCGR3A/B       NM_000570.4         325          145
524   Endogenous        STAT1       NM_007315.3        2167          456
525   Endogenous         CTSS       NM_004079.3         430          385
526   Endogenous         PDK1       NM_002610.3         435          252
527   Endogenous        ITGAV    NM_001144999.2         612         1041
528   Endogenous       ANGPT1    NM_001199859.1          21           53
529   Endogenous        BCL6B       NM_181844.3          15           43
530   Endogenous         CDH2       NM_001792.3          48           35
531   Endogenous        CSF3R       NM_000760.3         166          124
532   Endogenous         RELB       NM_006509.3          82           56
533   Endogenous       CXCL16    NM_001100812.1         109          124
534   Endogenous         IL6R       NM_000565.3          27           71
535   Endogenous        PDGFA       NM_033023.4          35           47
536   Endogenous       PIK3R1    NM_001242466.1         119          173
537   Endogenous          HK1       NM_000188.2         499          292
538   Endogenous          AXL       NM_001699.4          65           75
539   Endogenous          HK2       NM_000189.4         658          329
540   Endogenous       PDGFRB       NM_002609.3         347          409
541   Endogenous         FADD       NM_003824.3          92          489
542   Endogenous         CD74    NM_001025159.2        2455         2542
543   Endogenous        RIPK2       NM_003821.5         124          176
544   Endogenous       CD45RB ENST00000367367.1          45           38
545   Endogenous          BAD       NM_004322.3          86           67
546   Endogenous          PKM    NM_001206796.2        5714         2857
547   Endogenous        KLRB1       NM_002258.2          15           20
548   Endogenous      ADORA2A       NM_000675.5         128           33
549   Endogenous        IFIT1    NM_001270930.1        1506          116
550   Endogenous        UBE2T       NM_014176.1          46           26
551   Endogenous        RPL23       NM_000978.3        3210         5939
552   Endogenous         ARG2       NM_001172.3          32           70
553   Endogenous       TGFBR2    NM_001024847.2         114          238
554   Endogenous       CRABP2    NM_001199723.1        2655         1783
555   Endogenous          BLK    NM_001330465.1          18           18
556   Endogenous        CCL14       NM_032962.4          41          416
557   Endogenous        CCNB1       NM_031966.2         421          135
558   Endogenous        STAT2       NM_005419.2         998          514
559   Endogenous        IKBKB    NM_001190720.2         238          260
560   Endogenous         ZEB2    NM_001171653.1         214          283
561   Endogenous       LRRC32       NM_005512.2          85          142
562   Endogenous      IL22RA1       NM_021258.2          33           33
563   Endogenous         ELOB       NM_007108.2          42           54
564   Endogenous        ITGA1       NM_181501.1          70           92
565   Endogenous         IL24    NM_001185158.1          20           20
566   Endogenous        PVRIG       NM_024070.3          49           41
567   Endogenous          RB1       NM_000321.2         252          229
568   Endogenous        SRP54    NM_001146282.1         170          175
569   Endogenous        ICAM3       NM_002162.3          90           79
570   Endogenous         CCR5       NM_000579.3          49           44
571   Endogenous        CTLA4    NM_001037631.2          25           19
572   Endogenous          GLS       NM_014905.4          68           69
573   Endogenous        ITGAE       NM_002208.4         120          219
574   Endogenous          MET       NM_000245.2         110           96
575   Endogenous        WNT3A       NM_033131.3          18           30
576   Endogenous         TYMP    NM_001113755.2         752          388
577   Endogenous        IFI16    NM_001206567.1         207          169
578   Endogenous          PVR    NM_001135768.2          68           77
579   Endogenous        P4HA2    NM_001017973.1         157          314
580   Endogenous        BRIP1       NM_032043.2          71           49
581   Endogenous         ESR1       NM_000125.2          23         1154
582   Endogenous         DAB2    NM_001244871.1         120          129
583   Endogenous        DUSP1       NM_004417.3         111          719
584   Endogenous         CD8B       NM_172213.2          30           31
585   Endogenous       ACVR1C       NM_145259.2          29           33
586   Endogenous         IL15       NM_000585.4          25           26
587   Endogenous      KIR3DL1    NM_001322168.1          19           21
588   Endogenous         CDH1       NM_004360.3        3142          758
589   Endogenous         HES1       NM_005524.2         267          152
590   Endogenous          IHH       NM_002181.2          18           28
591   Endogenous        CCL19       NM_006274.2          24           35
592   Endogenous           C2       NM_000063.5         107           44
593   Endogenous         TLR7       NM_016562.3          23           29
594   Endogenous        IL2RA       NM_000417.2          19           14
595   Endogenous       PRKAA2       NM_006252.3          27           62
596   Endogenous      COL11A2    NM_001163771.1          13           14
597   Endogenous    TNFRSF10D       NM_003840.4          22           30
598   Endogenous      SIGLEC8       NM_014442.2          13           15
599   Endogenous           PC       NM_000920.3         103          108
600   Endogenous        IL17A       NM_002190.2          24           20
601   Endogenous         GLI1       NM_005269.2          19           18
602   Endogenous         GNG4    NM_001098721.1          37           51
603   Endogenous         LDHB    NM_001174097.2         572          465
604   Endogenous         DTX4       NM_015177.1          78           29
605   Endogenous         CD3G       NM_000073.2          14           16
606   Endogenous       S100A8       NM_002964.4        2954           16
607   Endogenous      ZC3H12A       NM_025079.2          29           30
608   Endogenous         IER3       NM_003897.3         280          817
609   Endogenous          CD4       NM_000616.4          29           33
610   Endogenous      S100A12       NM_005621.1          21           18
611   Endogenous          CD6    NM_001254751.1          16           22
612   Endogenous        CD163       NM_203416.2         144           83
613   Endogenous        DUSP2       NM_004418.3          22           25
614   Endogenous        HERC6    NM_001165136.1         158           56
615   Endogenous         MRC1       NM_002438.2          23           64
616   Endogenous         DLL4       NM_019074.2          36           53
617   Endogenous       SAMSN1    NM_001256370.1          63           69
618   Endogenous         CD28    NM_001243077.1          19           41
619   Endogenous         TAP2       NM_018833.2         321          120
620   Endogenous         ICOS       NM_012092.3           6           14
621   Endogenous      TNFSF12       NM_003809.2          45          100
622   Endogenous       IFITM2       NM_006435.2         956          569
623   Endogenous        DNMT1    NM_001130823.2         319          236
624   Endogenous       TNFSF8       NM_001244.3          32           28
625   Endogenous        TGFB2    NM_001135599.3          48           49
626   Endogenous      TMEM140       NM_018295.3          64           41
627   Endogenous      COL11A1       NM_001854.3         514          133
628   Endogenous       GIMAP6       NR_024115.1          20           40
629   Endogenous         IRF4       NM_002460.1          33           79
630   Endogenous        BNIP3       NM_004052.3         445          240
631   Endogenous         FPR3       NM_002030.4         225           79
632   Endogenous        HLA-C       NM_002117.4        1786          695
633   Endogenous        VEGFC       NM_005429.4         135           69
634   Endogenous      SIGLEC1       NM_023068.3          58           66
635   Endogenous          BID       NM_001196.3          40           34
636   Endogenous       MAPK10    NM_001318067.1          62           76
637   Endogenous         FCN1       NM_002003.4          16           24
638   Endogenous        H2AFX       NM_002105.2          71           33
639   Endogenous         CBLC    NM_001130852.1          34           35
640   Endogenous        CASP3       NM_032991.2         224          225
641   Endogenous        PIAS4       NM_015897.2         200           62
642   Endogenous      HLA-DRA       NM_019111.3        1430         2507
643   Endogenous        ULBP2       NM_025217.2          19           24
644   Endogenous        CASP1       NM_001223.4          71           77
645   Endogenous        MS4A2       NM_000139.3          18           19
646   Endogenous      HSD11B1       NM_181755.2          21           24
647   Endogenous         GAS1       NM_002048.2          47           41
648   Endogenous         FUT4       NM_002033.3          41           42
649   Endogenous         CSF1       NM_000757.5          59           71
650   Endogenous       FAM30A       NR_026800.2          23           25
651   Endogenous        ITPK1    NM_001142593.2         273         1750
652   Endogenous        BCAT1       NM_005504.6          81           26
653   Endogenous         CD80       NM_005191.3          43           20
654   Endogenous         C1QB       NM_000491.3         302          312
655   Endogenous         RELN       NM_005045.3          18           27
656   Endogenous        ICAM5       NM_003259.3          16           14
657   Endogenous        MAML2       NM_032427.1          39           53
658   Endogenous         OLR1       NM_002543.3         107           73
659   Endogenous       NFKBIE       NM_004556.2          58           43
660   Endogenous        WNT11    XM_011545241.2          20           19
661   Endogenous       LILRA3    NM_001172654.2          28           31
662   Endogenous     TNFSF13B    NM_001145645.2          51           81
663   Endogenous         TDO2       NM_005651.3         102           27
664   Endogenous       MAP3K5       NM_005923.3          64          125
665   Endogenous        HLA-F    NM_001098479.1         303          151
666   Endogenous         CD3E       NM_000733.3          28           42
667   Endogenous         RRM2       NM_001034.1         714           44
668   Endogenous           C7       NM_000587.2          33           81
669   Endogenous     TNFRSF14       NM_003820.3         203          197
670   Endogenous        FCGRT       NM_004107.4         216          403
671   Endogenous         WNT2       NM_003391.2          41           24
672   Endogenous         MICB       NM_005931.3          40           21
673   Endogenous        HMGA1       NM_145902.2         253          110
674   Endogenous        IL21R       NM_021798.3          19           13
675   Endogenous       CD300A    NM_001256841.1          38           34
676   Endogenous       TWIST1       NM_000474.3         160           93
677   Endogenous        IL1RN       NM_000577.3          34           19
678   Endogenous        CXCL1       NM_001511.3          18            9
679   Endogenous        SFXN1    NM_001322977.1         662         1899
680   Endogenous         GNLY       NM_012483.3          11           36
681   Endogenous         NID2       NM_007361.3         231          168
682   Endogenous      NECTIN1       NM_002855.4         180           90
683   Endogenous     SERPINA1    NM_001127702.1         164         1414
684   Endogenous        PDGFB       NM_002608.2          45           51
685   Endogenous        HLA-B       NM_005514.6        4911         2885
686   Endogenous        VCAM1       NM_001078.3         190          124
687   Endogenous     HLA-DPB1       NM_002121.5         383          805
688   Endogenous      HLA-DOA       NM_002119.3          29           49
689   Endogenous         GBP2       NM_004120.4         128           77
690   Endogenous          ATM       NM_000051.3         343          396
691   Endogenous        PSMB8       NM_004159.4         275          176
692   Endogenous         MLH1       NM_000249.2         173          132
693   Endogenous        PLA1A       NM_015900.2          23           31
694   Endogenous         NT5E       NM_002526.3         109           52
695   Endogenous        PALMD       NM_017734.4          23           74
696   Endogenous         UBA7       NM_003335.2         148           83
697   Endogenous       PIK3CD    NM_001350234.1          36           36
698   Endogenous         NOD2       NM_022162.1          36           40
699   Endogenous      CEACAM3    NM_001277163.2          33           39
700   Endogenous        RIPK3       NM_006871.3          43           76
701   Endogenous        IL1R2       NR_048564.1          16            6
702   Endogenous         JAK1       NM_002227.1         316          413
703   Endogenous         ENO1       NM_001428.3        5271          843
704   Endogenous       LILRA1    NM_001278318.1          27           23
705   Endogenous         BBS1       NM_024649.4          83           97
706   Endogenous        MYD88       NM_002468.3         214          176
707   Endogenous        CXCR3    NM_001142797.1          13           20
708   Endogenous         CD1C       NM_001765.2           9           22
709   Endogenous         TLR9       NM_017442.2          20           28
710   Endogenous         CCL7       NM_006273.3          67           23
711   Endogenous         CPA3       NM_001870.2          68          142
712   Endogenous       SH2D1A    NM_001114937.2          20           29
713   Endogenous         CCR4       NM_005508.4          33           24
714   Endogenous        HDAC4       NM_006037.3          46           33
715   Endogenous        POLD1    NM_001256849.1          44           41
716   Endogenous       PTPN11    NM_001330437.1         610          922
717   Endogenous         JAK2       NM_004972.2         152          236
718   Endogenous       WNT10A       NM_025216.2          17           16
719   Endogenous        ITGB2       NM_000211.3         166          174
720   Endogenous         TYMS       NM_001071.1         269           45
721   Endogenous        KAT2B       NM_003884.4         125          310
722   Endogenous        ITGA6    NM_001316306.1          65          246
723   Endogenous        TBX21       NM_013351.1          24           28
724   Endogenous        BRCA1       NM_007294.3          42           70
725   Endogenous      COL17A1       NM_000494.3          51           35
726   Endogenous        BIRC3       NM_001165.4          20           31
727   Endogenous         KRAS       NM_004985.3         151          181
728   Endogenous       IL11RA       NM_147162.1          39           89
729   Endogenous        SIRPA    NM_001040023.1         101           98
730   Endogenous        CEBPB       NM_005194.3         357          267
731   Endogenous        VTCN1    NM_001253849.1         755           68
732   Endogenous         SGK1       NM_005627.3         161          110
733   Endogenous        NLRC5       NM_032206.4         135           66
734   Endogenous         CCL8       NM_005623.2         271           46
735   Endogenous        TRAF1    NM_001190945.1          25           82
736   Endogenous       ADAM12       NM_003474.5         523          104
737   Endogenous        MMRN2       NM_024756.2          61          121
738   Endogenous        PTGS2       NM_000963.1          29           40
739   Endogenous        SMAD5       NM_005903.5         224          685
740   Endogenous          LCK       NM_005356.4          34           46
741   Endogenous        ITGB3       NM_000212.2          45           73
742   Endogenous       FCGR2B    NM_001002273.1          99           88
743   Endogenous         NRAS       NM_002524.4         294          248
744   Endogenous         IL34    NM_001172771.1          40           55
745   Endogenous        LAMA1       NM_005559.3          57           43
746   Endogenous       CLEC4E       NM_014358.3          34           33
747   Endogenous       IL18R1    NM_001282399.1          40           37
748   Endogenous         MFNG       NM_002405.3          98           29
749   Endogenous       TTC30A       NM_152275.3         124          170
750   Endogenous    TNFRSF10C       NM_003841.3          73           54
751     Positive     POS_C(8)      ERCC_00002.1        3852         4739
752     Positive   POS_A(128)      ERCC_00117.1       36727        43726
753     Positive POS_F(0.125)      ERCC_00034.1          75           85
754     Positive     POS_D(2)      ERCC_00092.1         725          898
755     Positive    POS_B(32)      ERCC_00112.1       14523        17129
756     Positive   POS_E(0.5)      ERCC_00035.1         150          158
757     Negative     NEG_C(0)      ERCC_00019.1          27           29
758     Negative     NEG_D(0)      ERCC_00076.1           8           15
759     Negative     NEG_E(0)      ERCC_00098.1          24           20
760     Negative     NEG_A(0)      ERCC_00096.1          17           29
761     Negative     NEG_H(0)      ERCC_00154.1          12           11
762     Negative     NEG_G(0)      ERCC_00144.1          14            7
763     Negative     NEG_F(0)      ERCC_00126.1          39           39
764     Negative     NEG_B(0)      ERCC_00041.1          20           17
765 Housekeeping          UBB       NM_018955.3        3440         4712
766 Housekeeping         PUM1    NM_001020658.1         615          750
767 Housekeeping         TLK2       NM_006852.3         144          418
768 Housekeeping      DNAJC14       NM_032364.5         201          244
769 Housekeeping        SF3A1       NM_005877.4         315          313
770 Housekeeping       POLR2A       NM_000937.2         460          550
771 Housekeeping         SDHA       NM_004168.3         339          570
772 Housekeeping      STK11IP       NM_052902.2         103          100
773 Housekeeping        NRDE2       NM_017970.3         179          336
774 Housekeeping          TBP    NM_001172085.1         117          230
775 Housekeeping         OAZ1       NM_004152.2        2242         1825
776 Housekeeping     TBC1D10B       NM_015527.3          92           86
777 Housekeeping         GUSB       NM_000181.1         146          177
778 Housekeeping        PSMC4       NM_006503.2         209          359
779 Housekeeping         TFRC       NM_003234.1         489          142
780 Housekeeping        ABCF1       NM_001090.2         170          258
781 Housekeeping        TMUB2       NM_177441.2          82          172
782 Housekeeping       MRPL19       NM_014763.3         232          223
783 Housekeeping         G6PD       NM_000402.4          92          199
784 Housekeeping        ERCC3       NM_000122.1         454          403
    pre_count_2 post_count_2 pre_count_3 post_count_3 pre_count_4 post_count_4
1           324           23        1465           24          87           13
2          2138          570         529          105          55          102
3            31           49          35            9         110           12
4           135          751         123          103          31           40
5          5611        15209        8545         3362        1618         2285
6          1564          361         257          197          73          129
7          3997         3936        2597          566         232          121
8            83           97         124           38          46           54
9          4795         5862        7387          779         888          882
10          470          388         292           65         107          122
11          167           59         219           52          32          216
12           10           20          11           16          12           12
13           85           68          26           21          20           31
14         1110          872        1059          236          75          142
15         4017         2217        2339         1203         467          534
16          746           85          36          166          33           34
17         1756         1347         799          349         512          122
18          452           21         798          145          27           31
19          184           54         105           24          16           25
20          266          247         424           92          45           70
21           18           36          23            7          25           11
22           50           45          47           51          25           43
23          476          580         974           88         263          122
24          751          876         863          315         189          284
25          187          614         645           33          78           61
26           57           86         106           13          27           22
27         1844         3676        2301          522         346          334
28          247          284         304           68          98           92
29          610          629         899          206         287          149
30           66           31          17           24          12           17
31          410          328         189           53          40           33
32           72           96         116           20          16           23
33          281         1309        1339          391         472          433
34         2115         1703        2727          545         700          738
35         3245         4603        3999         1976        1167         1515
36         4334        14695        8730         3523        1809         2069
37           78          194         332           45         149           53
38          777          526         892          202         287          175
39        26951        12249       20207         3808        4053         4854
40         1414         1819        3115          629        1002         1826
41          626          385         438          167          36           81
42          735          343         514           93         127          114
43         7977          783        4406          675         582          414
44          627          415         381           88         114           74
45           81          170         294          127         297          154
46          424          226         197           47          96          118
47          464          339         225          127         121           52
48           42           77          61           17          19           22
49          285          119         230           41          38           55
50          564          385         484          109          63           55
51          471         1063        1112          152         235          180
52           31           21          14            7           8           12
53         1446         1225        2188          474         871          362
54           73           57          49           11          30          138
55          149          134         247           40          20          181
56           83           15          10           16          23           11
57           32           17          30           20          23           15
58           96          114          86           14          20           16
59         1499          974         970          435         441          284
60           36           49          94           22          59           17
61          116           65          48           21          43           28
62          802         1827        1883          195         175          199
63          175          193         282           78          82           78
64         1731         1722        1377          188          84          166
65           67          108          78           23          34           45
66          693         1869        1591          237        1220          276
67          696          370         310           68          43           94
68          214          662         322           41          67           64
69          233          537         435           45          44           38
70           36           43          35           28          32           42
71           74          122         108           44         112           61
72          119          266         192           50          29           33
73           16           28          15           13          15           20
74          227           92          64           57          31           80
75           49           38          64           28          19           17
76          268          308         493           56         246           93
77          385          180         182           43          64           39
78          384          280         430           43          37           49
79          101          326         150           45          80           47
80          578         2098        1190           90         102          228
81          664          498         549          107          68           97
82         1535         1133        1784          259         332          268
83          125           95         105           29          28           31
84           23           35          47           26          90           12
85         1231          908        1167          251         285          109
86          450          527        1634          215         106          173
87           27           56          44           14          25           22
88         1068          338         222           95         268          234
89         1238         1428        5217          909        3675          599
90          967         1147        1404          501         377          135
91          146          113         315           56          42          219
92         2011           83          14           16          11           20
93          630         1101         944          164         122          197
94          386          123          41           53          27           43
95          681          574         695          151         234          202
96          200          271         409          101         170           64
97            8           15          10           20          20           15
98          249          108         135           76          41           36
99          177           23          11           25          11           17
100          49           45          29           17          17           16
101         170          121         149           33          75           42
102         327          239         526           53         349          108
103        2299         3846        3535          458         372          589
104        1081          585         904          154         110          141
105          97           21          25           24          32           16
106        4796         3354        4470          628        1618          996
107         877          657         790          182         165          292
108         761          529         668          220         242          191
109         900         1884        1322          247         261          170
110          52           50          71           13          34           15
111          21           38          22           19          13           14
112         109          176         166           36          29           29
113         859          894        1205          165         438          262
114          60          132         133           42          63           40
115         398          605         638          103         238           51
116         714          812        1063          190          96          110
117          37          118         256           85          30           28
118         771          628         409          160         375          333
119          14            5          10            9          13            8
120         151          252         319          307         136          153
121          36           50          56           33          22           20
122         117          136         126           63         137          115
123         162          389         143           77          38           79
124         521          398         292          130         148          162
125         366          228        1456          180         127          151
126        3528         3515        2733          331         328          692
127         105          119          95           48          49           39
128        1097         1712        1079          243         265          183
129         734          571         528          165          92           71
130         396           81          30          246         316          246
131        5314         5481        6963         1103        1624         1571
132        1250         1297        1350          254         300          295
133          14          273          95           37          28           35
134         708          730         865          154         267          166
135        2527         2266        2502          327         186          201
136         278          199         238           87          94           49
137         236          153         274           17          24           35
138          21           88         154           15          83           18
139         437          143         263           52          63           44
140         349          449         372           86         135           97
141        1134         1061         948          231         310          240
142         228          108          40           49           9            8
143          33           64          24           14          13           19
144          19           20          16           14           7           10
145          41          114          81           18          16           21
146         491          425         483           87         134           87
147        2862            7        7191         1853           5         1507
148       10375         4901       27761         1922        3855         1029
149          59           60          81           14          67           26
150         405          606         678           81         373          210
151         902         1614        1147          220         370          386
152        1113          307         734          322         275         1479
153        1133          806        1553          672         916          569
154          27           24          28           22          11           31
155         578          596         218          232         150          127
156         441          448         474           53          61           31
157         163           90         222           52          40           41
158         358          336         277           85          59           51
159         855          384         475           50          46           36
160          53           81          94           29          26           23
161         247          354         341          113         119           64
162          46          612        1018          439         184          458
163       11399        14987        7569          624         537         1077
164          30           52          45           36          23           14
165         721          616         703           78          64          103
166         462         1873        2797          320         383          241
167          14           17          10            8          15           26
168         724          776         730          112         168          120
169          46          158          63           28          35           27
170         103           95          78           18          38           19
171        1675          214         301           68          99          836
172         292          676         290           35          97           69
173         210          179         122           41          80           78
174        1111          802        1017          232         185          248
175          48          121         197           24          34           26
176        5387         7254        2081          773        1784          897
177        1744         1202         258           34         263          248
178         420          294         477           65          48           55
179          84           76         150           27          97           27
180         273          385         309           67         302           90
181          19          475         139           27         428          102
182         273         1681         976          190        1341          415
183        1310         1246        1476          296         293          244
184          43           14          11            9           5            3
185          71           77          74           12          26           15
186        1445         1817        1500          416         433          317
187         123          242         125           34          37           17
188        2058         1996        2131          380         297          287
189         880          603         650          184         195          182
190         145          262         243           52          59           77
191        1862         1247        1061           89         398          231
192        1254         1533        1589          358         287          299
193         997          658         840          152         146          153
194          31          115         318           12          13           18
195        1455         3175        3176          196         465          263
196         625          327         362           88          67           26
197        5385        15560       12075         3021        1032         1817
198          39          161          93           41          15           46
199          13           26          11           16           7           12
200        1886         1515        2128          375         261          240
201          62          171         175           23          66           32
202          49           82         106           25         106           29
203         259          393         355          134         114           59
204         185          364         373           62          99           91
205          30           60          53            9          19           16
206         540          373         453          297          31           51
207         699          726        1046          233         321          263
208          16           19          12            6          10            7
209         702          757        1050          112         336          327
210         403          652         654          242         567          271
211        1609         1340        1532          477         592          283
212         480         1210         735           66          57           75
213         142         1067         439           59          52           37
214          85          135         131           23          34           23
215        5182         1560        5154          802        3620          809
216          22           55          48           11          64           26
217         107          396        1235           46        1304           93
218          38           52          90           11          43           24
219         306          631         426           38          32           24
220         179          281         535           29         130           29
221         150          378         729          117         157           94
222          39           30           8           15           5           17
223         363          538         577          132         120          109
224         128          527         187           49          24           27
225         132           77         146           25          18           11
226         212          196         301          168         138          156
227          45          161          90           10          23           11
228         235          125         154           23          83           52
229         205          171         164           53          11           22
230        1067         1169         595          346         222          255
231          79          511         262           48          62           72
232         106          125         150           23         100           27
233        1202         1009        1081          239         193          250
234        1028          533         370          196         204          179
235          73          196          17           12          61           22
236         230          322         439           95         172          117
237          21           20          28            8         262            9
238         137           87          63           28         107           53
239        4875         2120        2463          571         279          379
240         489          223         201           74          99           96
241          74           64          81           35          21           13
242          10           37          10           19          15           18
243          22          920          72         1070          92            3
244         596          124         899          254          34           30
245         161          233         174           22          25           15
246         797          179         431           60          52          102
247          18           19          27           18          13            7
248        1226         1453        1713          149          43           72
249          26           30          12           10          12           12
250         185          430         151           48         103           52
251         810         2838        3873          757         539          337
252         321          253         420          131         165          107
253         153          235         355           54         362           36
254         322          708         910          143         317          202
255        2305         2564        7421         2880        2838         1142
256        2735         2489        2454          525         550          985
257         137          103          61          165         155          142
258        1171          680        1026          142         103          143
259          15           14          14           12           8            7
260          13           18           7           11           8           12
261         616          515         374          112          62           55
262          77           81         133           46          72           42
263         390          220         396           61          95           88
264          26           31         130           16          12            8
265         166          243         186          146         101          108
266          86           90          50           67          62           80
267          16           33          13           45          44           36
268          26           39          42           27          48           46
269         126          196         278           96         213          121
270        1142         2239        1310          163         133          175
271          87          226         190           84         136           66
272         188          166         111           94          80           86
273          39           50         116           28         118           40
274         283          311         502          128         284          135
275         126          262         220           50          56           47
276         249          176         844          194          71           81
277          55           96         119           42         154           60
278         430         2283         912          242         285          252
279         289          576         665          204         145          124
280         693          724         410          123         127          140
281         840         5543        3269         1087         465          727
282          87          144         244           66         239           88
283        1223         1773        2169          307         446          219
284         978          690        1096          319         531          817
285         586          179          62           29          29           21
286         524          481         528          136         147          143
287        3795         3477        4876         1137        1313         1528
288          42           80         122           42          37           34
289          60          157         147           53          77           68
290        1563           49          13           85          19           43
291         166         1693         910          698         482          352
292         498          273         387          182          64          162
293          29           53          48           13          28           18
294          34           98          69           37          28           50
295        1262          892         765          206         278          191
296          23           59          49           26          22           27
297         886          850         442          118          54          119
298        4277        17657        4159         1212         332          377
299        2955          457         326          194          26           25
300         602          112          92           70          31           55
301         122          301         288           34          85           74
302           8           19          30           17          40           11
303        2172         2643        1762          389         511          453
304         497          275         277           52          52           39
305        1218          141         707          486          99          107
306         720          590         684          168         198          247
307       24913        25552       24990         3683       11795         5834
308         892          822         730          162         200          164
309          49           56          29           18          23           15
310        1561         1594        3080          547        4676          900
311          33           31          29           18           9           14
312           8           27          12            5           5            4
313         163          243          72           34          58           15
314          59          137         249           19         320           19
315         568          576        1239          151         121           71
316        2083         1589        1876          325        1273          799
317         462         3394         853          358         121          121
318        1623         6098        3180         1567          85          731
319        1069          168          72           94          37           58
320         132          144         201           36          60           83
321          69           28           9           13          13           14
322         183          162         177           55          88           51
323          17           59          46            7          23            7
324          59           87         113           31         175           28
325         553          175          78           56          20           17
326         968         1685        1381          128         248          299
327         173          309         858          221         403          119
328         331          214         191           34          29           51
329        1290          706        2169          328         349          522
330        3336        14237        6907          659         690         1234
331         709          910        1428          462         884          455
332        1256          710         323          124         115          125
333          61          162         104           22          26           23
334          44           33          18           20          16           27
335         309          658         371          239         137          174
336         174          303         365           62         107           73
337         395          862         111          174          44           30
338        4106         2986        4471         1196        1013          909
339         411          580         935          284         758          240
340         305          424         447           94         167           73
341         190          487         298           42         149           92
342        5618         3097        2605          752         714          553
343        2136         2282        3342          303         374          475
344        3679         1118        1834          547         561         1424
345         988          712         813          394         268          472
346         140          195         351           40         106           29
347         127          605         301          250          54          131
348          23           23          26           10          30           16
349        1175          788        1202          140         104          173
350        1590          644          56          217          48           69
351        1170         1367        1087          240         188          104
352         167          325         579          121         185           77
353          19           28          14            7           9           10
354       16503         4973        6063         1842        3129         2001
355          19           37          32           22          35           15
356         257          978         431           59         103           80
357        2178         1082        1461          760         505          545
358          90         1514         584          210         168          174
359         256          113          46           42          19           15
360          32           16          13           17          14           16
361        2183           41          15           46          16           14
362        4093          604         598          173         111          127
363         179          121         159           71          88           43
364         353         1164         486           75         112          111
365          78          101         113           17          18           18
366         287          575         978           89          32           36
367          91          834         176           23          67           34
368         906          881        1102          138         145          166
369         382         1005         506           50          76          102
370        4991         5671        3489          697         728          699
371         215          585         578          149         249          185
372        1431         1758        1176          271         511          379
373         528          404         575          185         189          318
374          14           24          18           17          15           16
375          48          151          83           16         117           28
376        2402         7712        4077          407        1377         1068
377         139          124         226           54          68           49
378         904         1055         692          297         394          342
379         496          357         280          109          72          141
380         977         3022        1572          516         319          367
381         526         1142         793          223         557          319
382        1701         2771        2433          578         557          481
383         130          184         296           31          90           34
384         146          107          35           29          69           40
385         120          448         607          192          77          134
386          58           87         147           21          43           15
387       15117        13803       10570         1390        2879         1351
388         570          131         291           41          59           25
389        1024         1289        1253          265         392          390
390          38           50          64           24          86           11
391          57           72          45           16          35           22
392           9           14          11           11          13           10
393         592          453         492          181         230          189
394          99           88         108           43          69           49
395         314          473         623           99         200           62
396        1191          736        1092          135         186          277
397          85          132         136           18          21           23
398          11           22          13           20           9           10
399         829         5853        1887          437        1530          273
400         207          336         451          131         156          107
401         290          132         281           96          70           37
402         107          321         162           25          40           42
403          16           95          22           23          34            8
404         637          705         660          153         145          145
405         131          137          81           26          31           25
406        5458        12843        7022          929        1253          911
407         762          746         900          255         406          511
408          33           46          28           23          15           23
409        6373          330         190           20         463           39
410          14           15          10            8          10            6
411        3846         5813       12715         1867        1853         1187
412        1890          995         534           92          71           62
413         463          428         947          212         269          196
414          26           31          47           12          21           17
415          16          118          61           39          17           16
416         480          433         500          253         199          236
417        2583         2351        3101          620         756          524
418         301          421         705           65         444           91
419         248          320         714           76         246           48
420         115           65          47           21          29           41
421          53          113         168           33         159           36
422         273           24         855          171         124           18
423          86          481         239           25          47           33
424          17           20          15           19          49           12
425         137          112         126           39          25           30
426         170          388         253           52          92           45
427          92          225         219           34          34           23
428         658          746        1094          106         128          139
429        1202          783        1165          165         239          583
430          31           54          50           17          73           30
431         228          277         515           89         458          145
432         298          241         285           67          69           58
433          59           37          22           65          16           12
434         885          626         988           93          93           81
435         264          157         212           66          48           38
436         222          211         219           50          40           93
437        1137         1405        2983          667        1068          582
438        7367          144         191          165          39           46
439          30           28          21           20          21           22
440        1273          664         932          304         448          289
441         540          329         486          123         119          156
442         741          955        1459          744         846          707
443        1472           54          79           67          31           83
444         632          147         178           93          40          190
445         117          212          91           31          30           45
446         460          897        1526          295         216          116
447          48          158          57           33          32           35
448          32           32           9           15          10           11
449         107          268         423          118         128          120
450        2127         2109        1160          489         504          434
451          14           14          14           15          15           19
452         382          273         242           71          85           75
453         355          517         138           67         155           42
454         764          703         725          219         510          348
455        1247         1620         999          586         836          295
456        1269         1261        1287          149         138          111
457          19           30          57           20          30           18
458         171          277         217           35          53           48
459         327          342         254           45          72           80
460        1581         3640        1674          513         358          126
461       13281         8295       11514         1698        2312         1657
462         127          126         104           44          46           25
463         727          545         542          250         200          111
464          24           55          42           14          23           16
465          92           64          25           29          23           28
466         902         1184        1370          183         255          213
467          19           20           5           13          13           14
468         554          364         153          160         182           40
469         392          260         344           68          70           88
470          27           40          46           16          21           10
471        1441          291         312           64          44           38
472        1541          482         920          136         111          101
473          14            9           5           15           2           16
474          25           21          19           24          19           19
475         382          249         355           83         109           67
476         634          578        1175          258         729          202
477         779          733        1050          244         192          232
478        4005         2944        3818          723         585          670
479         484          644         764          100         176          107
480          20           15          12           12          18           18
481         274          312         334           92         164           88
482         147           80          97           43          27           55
483          23           27          13           17          30           22
484         129          178         104           73          53           69
485       12692         8136        8567         2889        2092         2286
486        4075         1689        2716          555         423          394
487         909         1193        2124          171         132          127
488         615           89          62           33          40           66
489         550          678        1111          237         194          301
490         950          163         116          225          19          277
491         117          118          15           26          23           75
492         193          112         113           54          30          104
493          51           22          16           25          17           23
494          28           34          61           27         180           11
495          44           33         142           20          16           22
496         492          261         426          136          65           81
497         375          654         540          158         559          499
498          31          139          74          149          17           74
499          97          153         204           42          40           39
500         812          183         157           25          53           27
501          33           54          83           12          19           29
502         429          350         413           85          75           55
503         223          607         343          154         135          110
504          51           25          29           14          24           22
505        2032         1572        1467          477         235          232
506          55           14          18           22          12           22
507          92          172         120           15          13           27
508         123          326         234           46          72           34
509         111          215         275           42          76           25
510         155          115         171           38          29           33
511         583          442         448          189         113          895
512          28           59          53           16         171            7
513        1092         1228        2376          303         527          401
514         904          734        1154          338         273          309
515         432          351         406           78          61           45
516         405          530         478           61          60           72
517        2568         1689        2081          879         594          551
518         192          224         305           52         197           70
519         120           91          68           31         228           30
520         908          891        1056          306         198          270
521          47          120          58           11          27            9
522          53           66          50           31          31           20
523         441         1859        1846          381         351          318
524        3352         4220        4271          596        2080          895
525        1447         2863        2801          960        3944         1218
526         348          248         382          128         850          187
527        2623         3344        3345         1271         873         2022
528         114           99          53           29          30           43
529         114          113         144           28          21           40
530          45          530          76           41          38           42
531         403          423         422          140          88           92
532         272          408         481           94         109           79
533         756          607         976          292         275          173
534         193          157         278           52          78           36
535        1154          177         140           57          47           26
536        2252          715         951          233         153          253
537        2330         1311        2143          222         203          247
538         343          504         485          154          93          119
539         300          896         525           66         110          412
540        3181         3354        1977          571         309          387
541         607         3706         509          563          87           60
542       15993        15141       36135         6166        9687         3755
543         486          474         416          138         172          299
544         155          247         298           80         158           81
545         765          401         591           52          52          111
546        8733         8615        6035         1913        1167         1422
547          67           53          76           28          86           37
548          66          132         307           26          38           23
549         693         1752         743          107          60          215
550         102          389         146           33          41           38
551       16936         9301       12551         3335        3322         2815
552          86           81          86           54          28           24
553        1127          672         719          287         450          448
554        3664        12227       20241         2236         975          791
555           6           12          16           20          22           14
556        2421          243         435          161         247          542
557         309         1093         667           95         118           70
558        3581         3903        3599          819         874          752
559         601          483         811          158         112           98
560        1391         1165        1136          316         548          435
561         317          648         645          150         189          168
562          89           44          15           32          26           20
563         109          133         167           53          44           54
564         647          344         213           61          82           73
565          20           47           3           28          20           26
566         305          263         473           53          72           58
567         931         1088         854          352         454          269
568         468          424         600          108         196          196
569         311          376         531          124         276          113
570         116          163         262           72         252           55
571          22           76         151           30         116           25
572         692          717         602          105          77           51
573         456          644         380          175         298          158
574        1159           85          59          102          59           67
575          17           22           8           29          15           27
576        2964         5178        3311          421         638          647
577        1022          897         714          345         410          328
578         353          229         172           40          24           26
579         209          315         361          124         101           78
580         125          317         208           54          46          187
581        3720         2923        3282          182         863          754
582         711          658         729          234         226          228
583        1403          740         589          164         241          486
584          93           79         123           35          76           30
585          47           35         112           28          33           49
586          42           30          90           38          61           50
587          22           13          15           29          28           21
588        7733         8486        6465          276        1355         3140
589        2566         1989        1539          343         267           65
590          20           20          24           17          25           26
591         110          345         181           41          52           24
592          82          241         283           40         130           72
593          37           78          99           34          46           39
594          31           37          42           34          36           22
595         187           40         164           60          22           31
596          58           32           9           17          17            8
597          81           36          62           36          28           37
598          22           54          34           13          35           44
599        1023          166         294           51          44          101
600          77           53          13           26          22           24
601         124           51          33           35          21           28
602          17           63          14           16          16           25
603        2565          808         601          272         315          262
604         330          461         106           67          37           38
605          17           21          33           25          60           23
606         249           80          22           80          70          180
607         186          100         137           28          28           31
608        2538          812        2325          106         317           61
609         148          151         216           51          57           29
610          60           42           8           32          21           44
611          68          122         248           46          76           31
612         462          729         331           80         289          605
613          73           45          45           22          28           29
614         376          374         157           66          59           67
615         320           96         102           97         201          201
616         252          179         153           33          41           40
617         114          556         408          113         383          137
618          80           91         264           54          68           25
619         860          749         788          115         255          173
620          17           52          84           25          78           22
621         692          776         728          142          95           85
622        2987         4922        4443          953         602         1085
623        1553         1391        1267          306         269          215
624          49           85         101           30          42           35
625         246          123         314          248          88           58
626         176          283         245           48          91           56
627          41         6891        3184         1455         513         1000
628         231          117         123           38          68           60
629         103          214         174           47         673           37
630         332          221         354          209         135          150
631         231          857         511          138         394          255
632        6150         4264        7607          575        1252          644
633         307          305         265           85         133          113
634         296          487         439           43          40           70
635         196          144         193           71          53           30
636         113           32          35           34          26           22
637         118           40          42           30          32           29
638         163          196         163           36          52           67
639          82          130         217           29          22           21
640         670          680         844          195         399          157
641         597          593         896          116          81          108
642        6505         6785       16375         5762       10826         4397
643          57           68          46           29          18           20
644         368          214         407          102         177           95
645          66          284          94           29          53           26
646          39           30          27           18          22           25
647        1034          869         289          128          40           65
648         163          208         231           60          53           47
649         812          317         639          138          80           78
650          50           46          27           23         137           21
651         818         1268         996          159         214          254
652          83          344         194           94          96           98
653          56          198         219           45          39           33
654        1642         2311        2848          575        1721         1326
655         419           25          19           21          19           27
656          63           18          19           33          17           23
657         385          156         131          101          56           61
658          59          755         664          203         178          252
659         143          179         153           49          70           47
660          70           34          44           61          27           24
661          15           14          18           21          25           32
662         174          176         216           77         143           65
663          26          157          44           29          63           45
664         613          177         421          215         127          155
665         666          490         593          140         205           95
666         106          146         206           63         149           65
667         451         1340         766          108         223          195
668         156           58         110           23          79          117
669        1726          829        2747          196         265          237
670        2857         3464        1718          343         379          303
671         100           99          47           29          89           27
672         165          244         380           40         109           72
673         642          759        1607          100          91           95
674          16           38          48           17          38           17
675         148          189         194           71          45           43
676          97          138          51           35          14           25
677         141           74          35           26          18           15
678         199           40           8           15          19           13
679         732          760         732          305         285          313
680         134           84         228           34         197           26
681         565         1442         974          477         182          327
682        2622          549         605          187         114          160
683        8474          133         222          226         225           95
684         119          200         146           30          27           21
685       29639        22468       24741         3051        6006         3822
686         625          713         324          136         286          131
687        3055         2714        7874         2692        4927         2049
688         105          112         248           72          93           50
689         430          525         545          185         287          109
690        1465          845        1719          487         620          449
691        1017          838        1179          126         412          230
692         799          779         533          162         165          129
693          36           35         434           40          42           37
694         289          432         201           83          95           92
695         575          162         139           87          53          120
696         620          532         627          165         143           87
697         142          111         153           40          54           28
698         137           88         380           41          80           33
699          26           15          25           30          23           35
700          90          112         180           33          70           25
701          46           32          21           23          20           49
702        2933         1219        2159          524         377          464
703        8845         2938        4519         1029         655          855
704          51           55          89           38          37           28
705         406          169         310           96          70           89
706        1092         1135        1248          160         148          136
707          32           55         113           28          39           23
708          68           25          49           41          15           19
709          45           61          40           39          35           29
710          44           69          17           26          19           21
711         288         1846         416          245         961          111
712          37           72         101           35          75           47
713          55          108         204           54         104           35
714         269          176         305          106          51           89
715         147          175         165           40          35           33
716        2215         1690        1767          452         455          404
717        2467          967        1219          290         414          254
718          44           47          59           28          68           28
719         752         1675        1344          452         380          240
720         412          634         342           83          99           84
721        1221          571         997          227         392          488
722        1882          448         855          187         397          497
723          28           29          42           41          31           24
724         163          255         185           51          52           30
725        4401          151          18          321          31           47
726          65           43          60           30          44           26
727         979          658         591          141         196          153
728         585          127         164           82          51           42
729         630          445         451          185         172          164
730        2224         1065        1124          345         293          373
731        2273          701         332         1702         276           87
732        1200          830         814          266         252          227
733         240          371         506           93         127           97
734         131          257          88           61         124           78
735         204          298         608           98          65           46
736        1374         2706        1901          869         436          381
737         616          246         177           82          96          117
738         129           72          16           47          40           38
739        1463          956        1387          369         280          200
740          92          157         258           57         154           50
741         128           83          64           72          50           63
742         220          413         598          199         452          364
743        1238         1228        1248          330         290          262
744         297           67          76           63          50           44
745         240          102          28           89          54           57
746          72           76          21           41          38           41
747          43           79          50           42          75           61
748         119          106         120           27          51           47
749         364          344         685          125         126          129
750         302           73         339           82         107           74
751        2453         2224        1729         4504        3552         4425
752       27681        23254       17945        42598       31296        38967
753          46           66          50           88          57           84
754         470          503         338          925         602          845
755       10228         8647        6685        16351       13062        16298
756         103           88          70          169         139          189
757          13           22          11           20          26           31
758          17           14          15           18          21           16
759          16           26          14           20          27           22
760          12           12           7           20          12           17
761          11           21          17           14          19            9
762           7           13           5           14          13           17
763          19           17          17           38          29           26
764          10           18          12           35          32           33
765       13464        15704        9279         3538        5928         3098
766        3278         1478        2483          658         451          533
767         561          533         515          130         135          517
768        1057          972        1130          110         112          143
769        1616         1190        1164          260         227          327
770        3813         2452        2351          570         342          449
771        2417         2032        2642          467         286          425
772         470          359         633           80          79          120
773         589          369         587          171         159          134
774         737          411         541          211         195          117
775        7198         8339        7887         1315        2365         1823
776         578          594         503          111          54          115
777         979          638        1180          146         224          149
778        1253         1265        1665          140         205          205
779         971          389         707          248         207          184
780         901          870         976          163         187          162
781         628          527         633          125          55           88
782         771          675         645          211         200          169
783         336          342         317           61          48           87
784        1321         1163        1321          449         423          578
    pre_count_5 post_count_5
1            20           15
2           147          125
3            53           13
4            73          103
5          1997         4576
6           207          132
7           550          379
8            57           56
9          1662         1172
10          297          144
11           11           56
12           10           15
13           21           30
14          267          274
15          938          821
16           45           38
17          333          622
18           31           23
19           31           25
20           51           71
21           12           18
22           20           37
23          150          155
24          334          402
25           80           66
26           36           29
27          562          904
28           80           92
29          312          204
30           16           23
31           99           67
32           28           24
33          299          668
34          554          594
35         1440         2616
36         2091         6004
37           80           73
38          222          235
39         5099         4202
40          790          546
41           82           87
42          174          122
43         1686          613
44          111          153
45           96          125
46          157          139
47          177          100
48           31           28
49           50           57
50          143          112
51          232          243
52           11           16
53          396          421
54           12           66
55           88           48
56            9           17
57           18           21
58           22           19
59          400          476
60           34           30
61           25           34
62          283          375
63           93          112
64          169          182
65           26           32
66          357          547
67           75           55
68          159           72
69           43           52
70           22           25
71           65           70
72           44           62
73           18            9
74           36           41
75           18           25
76           91           77
77           37           46
78           38           38
79          113           78
80          533          447
81          108           96
82          671          344
83           20           38
84           24           12
85          341          257
86          184          157
87           25           20
88          233          326
89           13          637
90          684          643
91           42           37
92          334           15
93          228          173
94           50           64
95          299          238
96           73          108
97           15           15
98           83           68
99           13           14
100          17           28
101          59           38
102          95           87
103         696          430
104         204          188
105          39           26
106        1116         1037
107         360          225
108         332          242
109         271          239
110          49           20
111          18           17
112          26           47
113         166          253
114          31           70
115         149          113
116          82          306
117          31           45
118         869          375
119          13            6
120         109          241
121          21           33
122          92          107
123         141          187
124         174          284
125          58          108
126        1137          492
127          38          106
128         238          375
129         162          161
130         167           46
131        1623         1896
132         290          481
133         118           73
134         201          250
135         232          320
136         109          159
137          60           30
138          42           24
139          59           48
140         123          188
141         242          320
142          16           17
143          20           27
144           7            9
145          11           18
146         103          105
147          13            6
148        1633         1587
149          39           26
150         151          173
151         306          377
152         317          245
153         430          624
154          26           23
155         156          177
156          41           60
157          61           63
158          54          127
159          90           92
160          18           19
161          79           94
162         205          208
163        3674         2681
164          23           29
165          83          110
166         851          897
167          14           10
168         186          181
169          46           79
170          22           21
171          93          169
172          44           85
173          71           95
174         260          345
175          29           22
176        1612          803
177         227          937
178          44           51
179          39           47
180          91          140
181          76          124
182         245          621
183         357          345
184           8            6
185          19           25
186         637          733
187          39           50
188         493          531
189         274          225
190          34          120
191         623          134
192         396          698
193         179          223
194          14           25
195         264          815
196          80           76
197        3261         6280
198          28           46
199          17            8
200         379          365
201          42           47
202          43           43
203          67          137
204          68           89
205          12           13
206          43           84
207         219          297
208           6           11
209         452          343
210         309          437
211         546          829
212         206          234
213          90          127
214          32           20
215         475          961
216          24           20
217         135           82
218          32           21
219          46          241
220          55           32
221          79          107
222          22           18
223          92          151
224          29           45
225          18           25
226          98          155
227          18           17
228          60           45
229          51           29
230         662          622
231          70          118
232          33           53
233         210          379
234         184          162
235          40           17
236         121          123
237          51           29
238          47           44
239         427          756
240         191          167
241          32           23
242          20           20
243         797         1181
244          64           42
245          45           26
246         115           63
247          16            9
248          73          347
249          21           10
250         109          100
251        1984          896
252          68          130
253         134           92
254         171          257
255        1211         1833
256        1228          886
257         152          146
258         149          144
259           7           13
260           7            5
261          55           63
262          58           44
263          74           68
264          20            7
265         107          153
266          58           79
267          49           40
268          42           35
269         124          120
270         205          347
271          73          115
272         110          119
273          60           55
274         167          127
275          57           76
276          90           88
277          70           53
278         230          872
279         127          171
280         216          127
281         635         2215
282         115           84
283        1178          684
284         548          484
285         138           86
286         239          136
287        1245         1529
288          82           32
289          60           62
290          77           38
291         429         1482
292         108          134
293          20           21
294          34           50
295         385          469
296          51           21
297         178          114
298         914         2329
299         177          102
300         140           93
301          48           73
302          21           17
303         687         1039
304          71           83
305         214           96
306         158          235
307        5651         8227
308         224          259
309          20           17
310        1866          771
311          39           15
312          14            7
313          24           50
314          77           29
315         154          133
316         877          720
317         172          664
318        1148         1236
319         112           86
320          35           62
321          17           15
322          61           54
323          22           11
324          42           33
325          60           38
326         238          428
327          11          128
328          46           53
329         353          314
330        2349         2884
331         458          566
332         203          192
333          29           24
334          17           23
335         252          404
336          51           89
337         231          183
338        1018         1339
339         274          292
340         112          165
341         133           68
342         976          370
343         531          526
344         576          388
345         404          399
346          62           47
347         135          381
348          20           11
349         173          135
350        1678          450
351         184          262
352         117          149
353          10           12
354        4351         2747
355          24           19
356         168          121
357         554          538
358         109          464
359          19           24
360          16            8
361          54           36
362         253          236
363          96           71
364          87          327
365          15           22
366         208          153
367         102           94
368         269          207
369         632          482
370        1090          960
371         141          248
372         801          640
373         218          248
374          19           14
375          34           44
376        1034         2491
377          61           55
378         402          493
379         107          154
380         502         1285
381         248          375
382         600          953
383          56           61
384          80           77
385         131          233
386          39           21
387        4509         4491
388          44           45
389         746          462
390          16           47
391          16           31
392           9           11
393         222          255
394          42           27
395         129          176
396         194          215
397          33           29
398          11           17
399         734         1180
400         112          215
401          56           52
402          54           36
403          17           45
404         143          187
405          57           30
406        1325         1606
407         375          329
408          12           28
409         201           25
410           6           10
411         765         1407
412         160          135
413         193          210
414          16           21
415          33           61
416         171          224
417         786          735
418         147          124
419          75           72
420          58           44
421          68           47
422         119           50
423          33           53
424          13           14
425          30           39
426          64           79
427          40           38
428         144          150
429         482          304
430          40           33
431         166          120
432         105           93
433          20           23
434         109          108
435          72           52
436         101           50
437         579          706
438         307          182
439          22           32
440         431          396
441         162          126
442         423          535
443         104           66
444         546           89
445          78           48
446         256          289
447          82           47
448          13           26
449          69          121
450         454          559
451          22           23
452         137          102
453          90           76
454         334          286
455        1178          814
456         172          196
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459         137          109
460         221          523
461        2557         1484
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467          10            8
468         139          292
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471          45           85
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473           7           15
474          20           17
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477         195          228
478         758          582
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481         184           88
482          32           32
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484          80           82
485        2733         3255
486         468          589
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488         111           60
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491          33           31
492          83           47
493          17           26
494          53           34
495          15           44
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499          31           37
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505         405          516
506          28           12
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508          39           65
509          65           38
510          35           30
511         787          166
512          60           19
513         533          569
514         287          249
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516         167          110
517         426          850
518          60           91
519          61           46
520         452          440
521          35           16
522          51           39
523         107          729
524        1264         1251
525        2075         1687
526         201          142
527         979         1529
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530          51           57
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534          58           37
535          66           38
536         247          299
537         276          225
538         103          194
539         541          129
540         695          865
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542        4256         5368
543         137          157
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545          83           68
546        2512         2884
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548          41           36
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593          40           53
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596          21           17
597          31           34
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626          64           84
627         362         3524
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630         167          187
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632         670          731
633         150          169
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635          57           74
636          26           45
637          30           22
638          59           44
639          40           32
640         365          280
641         126          101
642        4299         5723
643          38           26
644         109          134
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646          30           22
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650          62           16
651         455          297
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653          42           89
654         664          967
655          17           33
656          22           19
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658          43          358
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660          19           30
661          32           32
662          78          115
663          86           54
664         179          128
665         212           92
666          89           63
667         374          227
668         301          111
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670        1134          605
671          24           94
672          45           59
673         106           79
674          12           21
675          48           75
676          22           20
677          25           24
678          13           20
679         622          447
680          41           31
681         339          741
682         207          130
683         186          127
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685        4081         3240
686         287          372
687        2321         2541
688          55           66
689         181          138
690         624          534
691         161          195
692         212          216
693          34           50
694         110          136
695          82           83
696         111          133
697          70           53
698          50           47
699          35           21
700          43           40
701          16           30
702         486          463
703        1153         1248
704          34           40
705          95           92
706         154          183
707          25           18
708          53           34
709          29           32
710          25           31
711         338          782
712          41           25
713          45           37
714          82           78
715          40           48
716         591          581
717         373          337
718          42           27
719         409          501
720         365          122
721         279          285
722         302          279
723          33           26
724          48           60
725         367          117
726          31           34
727         231          212
728          66           68
729         163          280
730         386          392
731         225          188
732         370          351
733         103          125
734          52          122
735          62           68
736         375         2032
737         173           97
738          31           43
739         348          477
740          92           64
741          75           52
742         237          342
743         392          416
744          69           46
745          63           69
746          54           45
747          58           57
748          45           38
749         128          218
750          64           63
751        4346         4501
752       37992        40969
753          93           82
754         820          864
755       15828        16719
756         169          167
757          24           31
758          22           18
759          24           16
760          12           19
761          16           15
762          14           14
763          41           36
764          21           32
765        7791         4718
766         667          653
767         486          151
768         191          153
769         267          313
770         596          572
771         365          481
772         120           95
773         237          220
774         321          254
775        1643         2122
776          97           98
777         166          177
778         374          216
779         258          184
780         289          194
781          81          121
782         290          280
783          83           71
784         547          586

Augmentation of the data

# Creating wide data frame
df_clean <- read.csv(here("data/02_dat_clean.csv"))

df_wide <- df_clean |>
  # replace outliers for pre and post_count columns
  replace_outliers_with_na("pre_count") |> 
  replace_outliers_with_na("post_count") |>
  rowwise() |> 
  # calculate means
  mutate(mean_pre = 
           round(mean(c_across(starts_with("pre_count")), na.rm = TRUE), 1), 
         mean_post = 
           round(mean(c_across(starts_with("post_count")), na.rm = TRUE), 1)) |>
  ungroup() |> 
  # fold change made of case/control
  mutate(log2_fold_change = log2(mean_post / mean_pre)) 

# save data
write_csv(df_wide, here("data/03_dat_aug_01.csv"))


# make a longer data frame with a row for each "count" variable
df_long <- df_wide |>  
  pivot_longer(
    cols = starts_with("pre_count") | starts_with("post_count"), # select count columns
    names_to = "treatment",  # new column for column names
    values_to = "count_value" # new column for values
  ) |> 
  mutate(log2_count_value = log2(count_value)) |> # calculate log2 of counts
  mutate(bin_treatment = case_when(
                          str_detect(treatment, "^pre") ~ 0, # change "pre" to 0
                          str_detect(treatment, "^post") ~ 1)) |> # change "post" to 1
  mutate(treatment = case_when(
                          str_detect(treatment, "^pre") ~ "pre", # change to "pre" 
                          str_detect(treatment, "^post") ~ "post"))

# save data
write_csv(df_long, here("data/03_dat_aug_02.csv"))

Descriptive statistics

{.absolute left=“0”}

{.absolute left=“0”}

Distribution of log2 fold change per class

Are there significance in the log2 fold change for some genes?

  1. Nest data
# read augmented datafile
mbc_log2_transformed <- read_csv(here("data/03_dat_aug_02.csv"))
mbc_log2_transformed_nested <- mbc_log2_transformed |> # define new tbl
  group_by(gene) |> # group by name
  nest() # nest data by each gene
  1. Fitting linear models
mbc_log2_transformed_nested <- mbc_log2_transformed_nested |> 
  mutate(model_object = map( # add a model_object column
    .x = data, # use data column as input
    .f = ~lm(formula = log2_count_value ~ bin_treatment, # model log2 transformed values based on treatment
             data = .x)))
  1. Tidying linear model results with confidence intervals
mbc_log2_transformed_nested <- mbc_log2_transformed_nested |> 
  mutate(model_object_tidy = map( # add a tidy model_object column
    .x = model_object,
    .f = ~tidy(x = .x,
               conf.int = TRUE,
               conf.level = 0.95)))
  1. Unnesting
estimates <- mbc_log2_transformed_nested |> 
  unnest(model_object_tidy) # unnest nested tbl
estimates
  1. Filtering and selecting treatment effects from linear model estimates
estimates <- estimates |> 
  filter(term == "bin_treatment") |> # choose only "treatment"
  select(gene, # select variables of interest
         p.value, 
         estimate, 
         conf.low, 
         conf.high) |> 
  ungroup() # ungroup tbl

Results

Comment: Explain q value vs p value forest plot

Results pt 2

Discussion

  • Where any genes significantly up or downregulated with this treatment?
  • What effect could removing outliers have on the findings?
  • How could the analysis be improved?